diff --git a/.changeset/1041-agents-runtime-resolver-all-cli.md b/.changeset/1041-agents-runtime-resolver-all-cli.md
new file mode 100644
index 000000000..6310097f6
--- /dev/null
+++ b/.changeset/1041-agents-runtime-resolver-all-cli.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 1045
+---
+**Agent SDK/state/commit steps now resolve `gsd-tools` on shim-only installs for every runtime** — source `agents/*.md` (`gsd-planner`, `gsd-executor`, `gsd-verifier`, `gsd-plan-checker`, …) invoked bare `gsd-tools …`, which fails with `command not found` on shim-only installs where the binary is only reachable as `<runtime-home>/gsd-core/bin/gsd-tools.cjs` and is not on `PATH`. The agent then silently skipped init/state/validate/commit ceremony. #725 fixed only Codex's conversion layer; the source agents were never migrated, so the bug persisted on Claude Code and every other runtime that consumes the source agents directly. All 12 `gsd-tools`-calling agents now carry the canonical multi-runtime `gsd_run` resolver (the same preamble the workflow launchers use — covering claude/codex/cursor/gemini/copilot/windsurf/augment/trae/qwen/cline/opencode/kilo/hermes/antigravity homes), `gsd-phase-researcher`'s stale claude-only resolver is upgraded to the canonical one, and the launcher-parity + bare-call regression guards are extended to `agents/` so no runtime can silently regress. (#1041)
diff --git a/agents/gsd-code-fixer.md b/agents/gsd-code-fixer.md
index 841e8b435..9628acfac 100644
--- a/agents/gsd-code-fixer.md
+++ b/agents/gsd-code-fixer.md
@@ -456,7 +456,8 @@ For each finding in sorted order:
 
 Use `gsd-tools query commit` with conventional format (message first, then every staged file path):
 ```bash
-gsd-tools query commit \
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run query commit \
   "fix({padded_phase}): {finding_id} {short_description}" \
   --files \
   {all_modified_files}
@@ -468,7 +469,7 @@ Examples:
 
 **Multiple files:** List ALL modified files after the message (space-separated):
 ```bash
-gsd-tools query commit "fix(02): CR-01 ..." --files \
+gsd_run query commit "fix(02): CR-01 ..." --files \
   src/api/auth.ts src/types/user.ts tests/auth.test.ts
 ```
 
diff --git a/agents/gsd-debug-session-manager.md b/agents/gsd-debug-session-manager.md
index 6da552d7f..b020461c2 100644
--- a/agents/gsd-debug-session-manager.md
+++ b/agents/gsd-debug-session-manager.md
@@ -93,7 +93,8 @@ Agent(
 
 Resolve the debugger model before spawning:
 ```bash
-debugger_model=$(gsd-tools query resolve-model gsd-debugger 2>/dev/null | jq -r '.model' 2>/dev/null || true)
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+debugger_model=$(gsd_run query resolve-model gsd-debugger 2>/dev/null | jq -r '.model' 2>/dev/null || true)
 ```
 
 ## Step 3: Handle Agent Return
diff --git a/agents/gsd-debugger.md b/agents/gsd-debugger.md
index 9db62ea44..404b7f831 100644
--- a/agents/gsd-debugger.md
+++ b/agents/gsd-debugger.md
@@ -1150,7 +1150,8 @@ mv .planning/debug/{slug}.md .planning/debug/resolved/
 **Check planning config using state load (commit_docs is available from the output):**
 
 ```bash
-INIT=$(gsd-tools query state.load)
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+INIT=$(gsd_run query state.load)
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 # commit_docs is in the JSON output
 ```
@@ -1168,7 +1169,7 @@ Root cause: {root_cause}"
 
 Then commit planning docs via CLI (respects `commit_docs` config automatically):
 ```bash
-gsd-tools query commit "docs: resolve debug {slug}" --files .planning/debug/resolved/{slug}.md
+gsd_run query commit "docs: resolve debug {slug}" --files .planning/debug/resolved/{slug}.md
 ```
 
 **Append to knowledge base:**
@@ -1199,7 +1200,7 @@ Then append the entry:
 
 Commit the knowledge base update alongside the resolved session:
 ```bash
-gsd-tools query commit "docs: update debug knowledge base with {slug}" --files .planning/debug/knowledge-base.md
+gsd_run query commit "docs: update debug knowledge base with {slug}" --files .planning/debug/knowledge-base.md
 ```
 
 Report completion and offer next steps.
diff --git a/agents/gsd-executor.md b/agents/gsd-executor.md
index 9f342f194..b5a33bb08 100644
--- a/agents/gsd-executor.md
+++ b/agents/gsd-executor.md
@@ -73,7 +73,8 @@ Before executing, discover project context:
 Load execution context:
 
 ```bash
-INIT=$(gsd-tools query init.execute-phase "${PHASE}")
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+INIT=$(gsd_run query init.execute-phase "${PHASE}")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
@@ -81,7 +82,7 @@ Extract from init JSON: `executor_model`, `commit_docs`, `sub_repos`, `phase_dir
 
 Also load planning state (position, decisions, blockers) via the SDK — **use `node` to invoke the CLI** (not `npx`):
 ```bash
-gsd-tools query state.load 2>/dev/null
+gsd_run query state.load 2>/dev/null
 ```
 If STATE.md missing but .planning/ exists: offer to reconstruct or continue without.
 If .planning/ missing: Error — project not initialized.
@@ -271,8 +272,8 @@ Do NOT continue reading. Analysis without action is a stuck signal.
 Check if auto mode is active at executor start (chain flag or user preference):
 
 ```bash
-AUTO_CHAIN=$(gsd-tools query config-get workflow._auto_chain_active 2>/dev/null || echo "false")
-AUTO_CFG=$(gsd-tools query config-get workflow.auto_advance 2>/dev/null || echo "false")
+AUTO_CHAIN=$(gsd_run query config-get workflow._auto_chain_active 2>/dev/null || echo "false")
+AUTO_CFG=$(gsd_run query config-get workflow.auto_advance 2>/dev/null || echo "false")
 ```
 
 Auto mode is active if either `AUTO_CHAIN` or `AUTO_CFG` is `"true"`. Store the result for checkpoint handling below.
@@ -397,7 +398,7 @@ If RED or GREEN gate commits are missing, add a warning to SUMMARY.md under a `#
 **Behavior-Adding Task detection** (the gate only fires when this predicate returns true): apply via the centralized verb instead of inlining the three checks:
 
 ```bash
-IS_BEHAVIOR_ADDING=$(gsd-tools query task.is-behavior-adding "$TASK_FILE" --pick is_behavior_adding)
+IS_BEHAVIOR_ADDING=$(gsd_run query task.is-behavior-adding "$TASK_FILE" --pick is_behavior_adding)
 ```
 
 The verb owns the canonical predicate (tdd="true" frontmatter AND `<behavior>` block AND non-test source files in `<files>`). Pure doc-only / config-only / test-only tasks return `false` and are exempt. Full result also exposes per-check breakdown (`checks.tdd_true`, `checks.has_behavior_block`, `checks.has_source_files`) and a human-readable `reason` — use these in the halt-and-report payload when the gate trips. See `references/execute-mvp-tdd.md` for halt protocol.
@@ -497,7 +498,7 @@ git add src/types/user.ts
 
 **If `sub_repos` is configured (non-empty array from init context):** Use `commit-to-subrepo` to route files to their correct sub-repo:
 ```bash
-gsd-tools query commit-to-subrepo "{type}({phase}-{plan}): {concise task description}" --files file1 file2 ...
+gsd_run query commit-to-subrepo "{type}({phase}-{plan}): {concise task description}" --files file1 file2 ...
 ```
 Returns JSON with per-repo commit hashes: `{ committed: true, repos: { "backend": { hash: "abc", files: [...] }, ... } }`. Record all hashes for SUMMARY.
 
@@ -674,32 +675,32 @@ After SUMMARY.md, update STATE.md using `gsd-tools query` state handlers (positi
 
 ```bash
 # Advance plan counter (handles edge cases automatically)
-gsd-tools query state.advance-plan
+gsd_run query state.advance-plan
 
 # Recalculate progress bar from disk state
-gsd-tools query state.update-progress
+gsd_run query state.update-progress
 
 # Record execution metrics (phase, plan, duration, tasks, files)
-gsd-tools query state.record-metric \
+gsd_run query state.record-metric \
   "${PHASE}" "${PLAN}" "${DURATION}" "${TASK_COUNT}" "${FILE_COUNT}"
 
 # Add decisions (extract from SUMMARY.md key-decisions)
 for decision in "${DECISIONS[@]}"; do
-  gsd-tools query state.add-decision "${decision}"
+  gsd_run query state.add-decision "${decision}"
 done
 
 # Update session info (timestamp, stopped-at, resume-file)
-gsd-tools query state.record-session \
+gsd_run query state.record-session \
   "" "Completed ${PHASE}-${PLAN}-PLAN.md" "None"
 ```
 
 ```bash
 # Update ROADMAP.md progress for this phase (plan counts, status)
-gsd-tools query roadmap.update-plan-progress "${PHASE_NUMBER}"
+gsd_run query roadmap.update-plan-progress "${PHASE_NUMBER}"
 
 # Mark completed requirements from PLAN.md frontmatter
 # Extract the `requirements` array from the plan's frontmatter, then mark each complete
-gsd-tools query requirements.mark-complete ${REQ_IDS}
+gsd_run query requirements.mark-complete ${REQ_IDS}
 ```
 
 **Requirement IDs:** Extract from the PLAN.md frontmatter `requirements:` field (e.g., `requirements: [AUTH-01, AUTH-02]`). Pass all IDs to `requirements mark-complete`. If the plan has no requirements field, skip this step.
@@ -717,13 +718,13 @@ gsd-tools query requirements.mark-complete ${REQ_IDS}
 
 **For blockers found during execution:**
 ```bash
-gsd-tools query state.add-blocker "Blocker description"
+gsd_run query state.add-blocker "Blocker description"
 ```
 </state_updates>
 
 <final_commit>
 ```bash
-gsd-tools query commit "docs({phase}-{plan}): complete [plan-name] plan" --files \
+gsd_run query commit "docs({phase}-{plan}): complete [plan-name] plan" --files \
   .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
 ```
 
diff --git a/agents/gsd-intel-updater.md b/agents/gsd-intel-updater.md
index 3e12f0cf7..9fd9a165b 100644
--- a/agents/gsd-intel-updater.md
+++ b/agents/gsd-intel-updater.md
@@ -212,7 +212,8 @@ Glob for project structure indicators:
 
 Read package.json, configs, and build files. Write `stack.json`. Then patch its timestamp:
 ```bash
-gsd-tools intel patch-meta .planning/intel/stack.json 
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run intel patch-meta .planning/intel/stack.json 
 ```
 
 ### Step 3: File Graph
@@ -221,7 +222,7 @@ Glob source files (`**/*.ts`, `**/*.js`, `**/*.py`, etc., excluding node_modules
 Read key files (entry points, configs, core modules) for imports/exports.
 Write `file-roles.json`. Then patch its timestamp:
 ```bash
-gsd-tools intel patch-meta .planning/intel/file-roles.json 
+gsd_run intel patch-meta .planning/intel/file-roles.json 
 ```
 
 Focus on files that matter -- entry points, core modules, configs. Skip test files and generated code unless they reveal architecture.
@@ -232,7 +233,7 @@ Grep for route definitions, endpoint declarations, CLI command registrations.
 Patterns to search: `app.get(`, `router.post(`, `@GetMapping`, `def route`, express route patterns.
 Write `api-map.json`. If no API endpoints found, write an empty entries object. Then patch its timestamp:
 ```bash
-gsd-tools intel patch-meta .planning/intel/api-map.json 
+gsd_run intel patch-meta .planning/intel/api-map.json 
 ```
 
 ### Step 5: Dependencies
@@ -241,7 +242,7 @@ Read package.json (dependencies, devDependencies), requirements.txt, go.mod, Car
 Cross-reference with actual imports to populate `used_by`.
 Write `dependency-graph.json`. Then patch its timestamp:
 ```bash
-gsd-tools intel patch-meta .planning/intel/dependency-graph.json 
+gsd_run intel patch-meta .planning/intel/dependency-graph.json 
 ```
 
 ### Step 6: Architecture
@@ -249,7 +250,7 @@ gsd-tools intel patch-meta .planning/intel/dependency-graph.json
 Synthesize patterns from steps 2-5 into structured JSON.
 Write `arch-decisions.json` with the JSON schema defined in the Intel File Schemas section above. Then patch its timestamp:
 ```bash
-gsd-tools intel patch-meta .planning/intel/arch-decisions.json
+gsd_run intel patch-meta .planning/intel/arch-decisions.json
 ```
 
 ### Step 6.5: Self-Check
diff --git a/agents/gsd-phase-researcher.md b/agents/gsd-phase-researcher.md
index 8df612a10..889243505 100644
--- a/agents/gsd-phase-researcher.md
+++ b/agents/gsd-phase-researcher.md
@@ -110,7 +110,8 @@ Construct a JSON file at a temp path (e.g. `/tmp/research-plan-input.json`):
 ### Step B — Obtain the fetch plan
 
 ```bash
-gsd-tools query research-plan --input /tmp/research-plan-input.json
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run query research-plan --input /tmp/research-plan-input.json
 ```
 
 Returns `{ "items": [ { "question": "...", "key": "<sha256>", "cache": { "hit": true/false, "stale": false }, "fetch": { "provider": "context7", "query": "..." } } ] }`.
@@ -145,7 +146,7 @@ For any other provider id `X` not listed above: use `mcp__X__*` if available, el
 After digesting a source, persist it so future runs can reuse it:
 
 ```bash
-gsd-tools query research-store put <key> \
+gsd_run query research-store put <key> \
   --content "<one-paragraph digest>" \
   --source <curated|web> \
   --provider <provider-id> \
@@ -162,9 +163,9 @@ gsd-tools query research-store put <key> \
 Obtain the confidence tier from code — do not hard-code tiers in your reasoning:
 
 ```bash
-gsd-tools query classify-confidence --provider <provider-id>
+gsd_run query classify-confidence --provider <provider-id>
 # for cross-checked findings, add --verified:
-gsd-tools query classify-confidence --provider <provider-id> --verified
+gsd_run query classify-confidence --provider <provider-id> --verified
 ```
 
 Returns `HIGH`, `MEDIUM`, or `LOW`. Use that value when tagging claims and when calling `research-store put --confidence <value>`.
@@ -197,7 +198,7 @@ emitting the `## Package Legitimacy Audit` section in RESEARCH.md.
 ### Step 1 — Run legitimacy check via seam
 
 ```bash
-gsd-tools query package-legitimacy check --ecosystem <npm|pypi|crates> <pkg1> <pkg2> ...
+gsd_run query package-legitimacy check --ecosystem <npm|pypi|crates> <pkg1> <pkg2> ...
 ```
 
 Returns a JSON array of per-package verdicts:
@@ -520,7 +521,7 @@ Orchestrator provides: phase number/name, description/goal, requirements, constr
 
 Load phase context using init command:
 ```bash
-INIT=$(gsd-tools query init.phase-op "${PHASE}")
+INIT=$(gsd_run query init.phase-op "${PHASE}")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
@@ -557,7 +558,6 @@ ls .planning/graphs/graph.json 2>/dev/null
 If graph.json exists, check freshness:
 
 ```bash
-_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
 gsd_run graphify status
 ```
 
@@ -781,7 +781,7 @@ Write to: `$PHASE_DIR/$PADDED_PHASE-RESEARCH.md`
 ## Step 7: Commit Research (optional)
 
 ```bash
-gsd-tools query commit "docs($PHASE): research phase domain" --files "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
+gsd_run query commit "docs($PHASE): research phase domain" --files "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
 ```
 
 ## Step 8: Return Structured Result
diff --git a/agents/gsd-plan-checker.md b/agents/gsd-plan-checker.md
index 35aaf5cf2..b46eb378a 100644
--- a/agents/gsd-plan-checker.md
+++ b/agents/gsd-plan-checker.md
@@ -655,7 +655,8 @@ issue:
 
 Load phase operation context:
 ```bash
-INIT=$(gsd-tools query init.phase-op "${PHASE_ARG}")
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+INIT=$(gsd_run query init.phase-op "${PHASE_ARG}")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
@@ -664,11 +665,11 @@ Extract from init JSON: `phase_dir`, `phase_number`, `has_plans`, `plan_count`.
 Orchestrator provides CONTEXT.md content in the verification prompt. If provided, parse for locked decisions, discretion areas, deferred ideas.
 
 ```bash
-gsd-tools query phase.list-plans "$phase_number"
+gsd_run query phase.list-plans "$phase_number"
 # Research / brief artifacts (deterministic listing)
-gsd-tools query phase.list-artifacts "$phase_number" --type research
-gsd-tools query roadmap.get-phase "$phase_number"
-gsd-tools query phase.list-artifacts "$phase_number" --type summary
+gsd_run query phase.list-artifacts "$phase_number" --type research
+gsd_run query roadmap.get-phase "$phase_number"
+gsd_run query phase.list-artifacts "$phase_number" --type summary
 ```
 
 **Extract:** Phase goal, requirements (decompose goal), locked decisions, deferred ideas.
@@ -680,7 +681,7 @@ Use `gsd-tools query` to validate plan structure:
 ```bash
 for plan in "$PHASE_DIR"/*-PLAN.md; do
   echo "=== $plan ==="
-  PLAN_STRUCTURE=$(gsd-tools query verify.plan-structure "$plan")
+  PLAN_STRUCTURE=$(gsd_run query verify.plan-structure "$plan")
   echo "$PLAN_STRUCTURE"
 done
 ```
@@ -698,7 +699,7 @@ Map errors/warnings to verification dimensions:
 Extract must_haves from each plan using `gsd-tools query`:
 
 ```bash
-MUST_HAVES=$(gsd-tools query frontmatter.get "$PLAN_PATH" must_haves)
+MUST_HAVES=$(gsd_run query frontmatter.get "$PLAN_PATH" must_haves)
 ```
 
 Returns JSON: `{ truths: [...], artifacts: [...], key_links: [...] }`
@@ -743,7 +744,7 @@ For each requirement: find covering task(s), verify action is specific, flag gap
 Use `verify.plan-structure` (already run in Step 2):
 
 ```bash
-PLAN_STRUCTURE=$(gsd-tools query verify.plan-structure "$PLAN_PATH")
+PLAN_STRUCTURE=$(gsd_run query verify.plan-structure "$PLAN_PATH")
 ```
 
 The `tasks` array in the result shows each task's completeness:
@@ -756,7 +757,7 @@ The `tasks` array in the result shows each task's completeness:
 
 **For manual validation of specificity** (`verify.plan-structure` checks structure, not content quality), use structured extraction instead of grepping raw XML:
 ```bash
-gsd-tools query plan.task-structure "$PLAN_PATH"
+gsd_run query plan.task-structure "$PLAN_PATH"
 ```
 Inspect `tasks` in the JSON; open the PLAN in the editor for prose-level review.
 
@@ -783,8 +784,8 @@ Missing: No mention of fetch/API call → Issue: Key link not planned
 ## Step 8: Assess Scope
 
 ```bash
-gsd-tools query plan.task-structure "$PHASE_DIR/$PHASE-01-PLAN.md"
-gsd-tools query frontmatter.get "$PHASE_DIR/$PHASE-01-PLAN.md" files_modified
+gsd_run query plan.task-structure "$PHASE_DIR/$PHASE-01-PLAN.md"
+gsd_run query frontmatter.get "$PHASE_DIR/$PHASE-01-PLAN.md" files_modified
 ```
 
 Thresholds: 2-3 tasks/plan good, 4 warning, 5+ blocker (split required).
diff --git a/agents/gsd-planner.md b/agents/gsd-planner.md
index fc4fc7999..5905ad140 100644
--- a/agents/gsd-planner.md
+++ b/agents/gsd-planner.md
@@ -123,37 +123,7 @@ If a feature has none of these three constraints, it gets planned. Period.
 
 <philosophy>
 
-## Solo Developer + Claude Workflow
-
-Planning for ONE person (the user) and ONE implementer (Claude).
-- No teams, stakeholders, ceremonies, coordination overhead
-- User = visionary/product owner, Claude = builder
-- Estimate effort in context window cost, not time
-
-## Plans Are Prompts
-
-PLAN.md IS the prompt (not a document that becomes one). Contains:
-- Objective (what and why)
-- Context (@file references)
-- Tasks (with verification criteria)
-- Success criteria (measurable)
-
-## Quality Degradation Curve
-
-| Context Usage | Quality | Claude's State |
-|---------------|---------|----------------|
-| 0-30% | PEAK | Thorough, comprehensive |
-| 30-50% | GOOD | Confident, solid work |
-| 50-70% | DEGRADING | Efficiency mode begins |
-| 70%+ | POOR | Rushed, minimal |
-
-**Rule:** Plans should complete within ~50% context. More plans, smaller scope, consistent quality. Each plan: 2-3 tasks max.
-
-## Ship Fast
-
-Plan -> Execute -> Ship -> Learn -> Repeat
-
-**Anti-enterprise patterns (delete if seen):** team structures, RACI matrices, sprint ceremonies, time estimates in human units, complexity/difficulty as scope justification, documentation for documentation's sake.
+See @~/.claude/gsd-core/references/planner-guidance.md for planning philosophy (Solo Developer workflow, Plans Are Prompts, Quality Degradation Curve, Ship Fast).
 
 </philosophy>
 
@@ -224,50 +194,7 @@ Every task has four required fields:
 - Good: "Valid credentials return 200 + JWT cookie, invalid credentials return 401"
 - Bad: "Authentication is complete"
 
-## Task Types
-
-| Type | Use For | Autonomy |
-|------|---------|----------|
-| `auto` | Everything Claude can do independently | Fully autonomous |
-| `checkpoint:human-verify` | Visual/functional verification | Pauses for user |
-| `checkpoint:decision` | Implementation choices | Pauses for user |
-| `checkpoint:human-action` | Truly unavoidable manual steps (rare) | Pauses for user |
-
-**Automation-first rule:** If Claude CAN do it via CLI/API, Claude MUST do it. Checkpoints verify AFTER automation, not replace it.
-
-## Task Sizing
-
-Each task targets **10–30% context consumption**.
-
-| Context Cost | Action |
-|--------------|--------|
-| < 10% context | Too small — combine with a related task |
-| 10-30% context | Right size — proceed |
-| > 30% context | Too large — split into two tasks |
-
-**Context cost signals (use these, not time estimates):**
-- Files modified: 0-3 = ~10-15%, 4-6 = ~20-30%, 7+ = ~40%+ (split)
-- New subsystem: ~25-35%
-- Migration + data transform: ~30-40%
-- Pure config/wiring: ~5-10%
-
-**Too large signals:** Touches >3-5 files, multiple distinct chunks, action section >1 paragraph.
-
-**Combine signals:** One task sets up for the next, separate tasks touch same file, neither meaningful alone.
-
-## Interface-First Task Ordering
-
-When a plan creates new interfaces consumed by subsequent tasks:
-
-1. **First task: Define contracts** — Create type files, interfaces, exports
-2. **Middle tasks: Implement** — Build against the defined contracts
-3. **Last task: Wire** — Connect implementations to consumers
-
-This prevents the "scavenger hunt" anti-pattern where executors explore the codebase to understand contracts. They receive the contracts in the plan itself.
-
-## Specificity
-
-**Test:** Could a different Claude instance execute without asking clarifying questions? If not, add specificity. See @~/.claude/gsd-core/references/planner-antipatterns.md for vague-vs-specific comparison table.
+See @~/.claude/gsd-core/references/planner-guidance.md for Task Types table, Task Sizing rules, Interface-First Task Ordering, and Specificity guidance.
 
 ## TDD Detection
 
@@ -336,47 +263,13 @@ Exceptions where `tdd="true"` is not needed: `type="checkpoint:*"` tasks, config
 
 **Compatibility with TDD detection:** When both `MVP_MODE=true` and `workflow.tdd_mode=true`, every behavior-adding task uses `tdd="true"` and a `<behavior>` block, AND the task ordering follows the vertical-slice structure above. The first task is always a failing end-to-end test.
 
-## User Setup Detection
-
-For tasks involving external services, identify human-required configuration:
-
-External service indicators: New SDK (`stripe`, `@sendgrid/mail`, `twilio`, `openai`), webhook handlers, OAuth integration, `process.env.SERVICE_*` patterns.
-
-For each external service, determine:
-1. **Env vars needed** — What secrets from dashboards?
-2. **Account setup** — Does user need to create an account?
-3. **Dashboard config** — What must be configured in external UI?
-
-Record in `user_setup` frontmatter. Only include what Claude literally cannot do. Do NOT surface in planning output — execute-plan handles presentation.
+See @~/.claude/gsd-core/references/planner-guidance.md for User Setup Detection protocol (external service indicators, env vars, dashboard config).
 
 </task_breakdown>
 
 <dependency_graph>
 
-## Building the Dependency Graph
-
-**For each task, record:**
-- `needs`: What must exist before this runs
-- `creates`: What this produces
-- `has_checkpoint`: Requires user interaction?
-
-**Example:** A→C, B→D, C+D→E, E→F(checkpoint). Waves: {A,B} → {C,D} → {E} → {F}.
-
-**Prefer vertical slices** (User feature: model+API+UI) over horizontal layers (all models → all APIs → all UIs). Vertical = parallel. Horizontal = sequential. Use horizontal only when shared foundation is required.
-
-## File Ownership for Parallel Execution
-
-Exclusive file ownership prevents conflicts:
-
-```yaml
-# Plan 01 frontmatter
-files_modified: [src/models/user.ts, src/api/users.ts]
-
-# Plan 02 frontmatter (no overlap = parallel)
-files_modified: [src/models/product.ts, src/api/products.ts]
-```
-
-No overlap → can run parallel. File in multiple plans → later plan depends on earlier.
+See @~/.claude/gsd-core/references/planner-guidance.md for dependency graph building rules and file ownership for parallel execution.
 
 </dependency_graph>
 
@@ -405,17 +298,7 @@ Plans should complete within ~50% context (not 80%). No context anxiety, quality
 
 **CONSIDER splitting:** >5 files total, natural semantic boundaries, context cost estimate exceeds 40% for a single plan. See `<planner_authority_limits>` for prohibited split reasons.
 
-## Granularity Calibration
-
-The resolved granularity is provided in the planning context as `**Granularity:** <value>`. Read that value and apply the corresponding row below. When no explicit value is present, default to Standard.
-
-| Granularity | Typical Plans/Phase | Tasks/Plan |
-|-------------|---------------------|------------|
-| Coarse | 1-3 | 2-3 |
-| Standard | 3-5 | 2-3 |
-| Fine | 5-10 | 2-3 |
-
-Derive plans from actual work. Granularity determines compression tolerance, not a target.
+See @~/.claude/gsd-core/references/planner-guidance.md for Granularity Calibration table (Coarse/Standard/Fine plans-per-phase).
 
 </scope_estimation>
 
@@ -773,7 +656,8 @@ start of execution when `--reviews` flag is present or reviews mode is active.
 Load planning context:
 
 ```bash
-INIT=$(gsd-tools query init.plan-phase "${PHASE}")
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+INIT=$(gsd_run query init.plan-phase "${PHASE}")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 ```
 
@@ -781,7 +665,7 @@ Extract from init JSON: `planner_model`, `researcher_model`, `checker_model`, `c
 
 Also load planning state (position, decisions, blockers) via the SDK — **use `node` to invoke the CLI** (not `npx`):
 ```bash
-gsd-tools query state.load 2>/dev/null
+gsd_run query state.load 2>/dev/null
 ```
 If STATE.md missing but .planning/ exists, offer to reconstruct or continue without.
 </step>
@@ -848,7 +732,7 @@ Apply discovery level protocol (see discovery_levels section).
 
 **Step 1 — Generate digest index:**
 ```bash
-gsd-tools query history-digest
+gsd_run query history-digest
 ```
 
 **Step 2 — Select relevant phases (typically 2-4):**
@@ -1037,7 +921,7 @@ Include all frontmatter fields.
 Validate each created PLAN.md using `gsd-tools query`:
 
 ```bash
-VALID=$(gsd-tools query frontmatter.validate "$PLAN_PATH" --schema plan)
+VALID=$(gsd_run query frontmatter.validate "$PLAN_PATH" --schema plan)
 ```
 
 Returns JSON: `{ valid, missing, present, schema }`
@@ -1050,7 +934,7 @@ Required plan frontmatter fields:
 Also validate plan structure:
 
 ```bash
-STRUCTURE=$(gsd-tools query verify.plan-structure "$PLAN_PATH")
+STRUCTURE=$(gsd_run query verify.plan-structure "$PLAN_PATH")
 ```
 
 Returns JSON: `{ valid, errors, warnings, task_count, tasks }`
@@ -1089,7 +973,7 @@ Plans:
 
 <step name="git_commit">
 ```bash
-gsd-tools query commit "docs($PHASE): create phase plan" --files \
+gsd_run query commit "docs($PHASE): create phase plan" --files \
   .planning/phases/$PHASE-*/$PHASE-*-PLAN.md .planning/ROADMAP.md
 ```
 </step>
@@ -1102,59 +986,7 @@ Return structured planning outcome to orchestrator.
 
 <structured_returns>
 
-## Planning Complete
-
-```markdown
-## PLANNING COMPLETE
-
-**Phase:** {phase-name}
-**Plans:** {N} plan(s) in {M} wave(s)
-
-### Wave Structure
-
-| Wave | Plans | Autonomous |
-|------|-------|------------|
-| 1 | {plan-01}, {plan-02} | yes, yes |
-| 2 | {plan-03} | no (has checkpoint) |
-
-### Plans Created
-
-| Plan | Objective | Tasks | Files |
-|------|-----------|-------|-------|
-| {phase}-01 | [brief] | 2 | [files] |
-| {phase}-02 | [brief] | 3 | [files] |
-
-### Next Steps
-
-Execute: `/gsd:execute-phase {phase}`
-
-<sub>`/clear` first - fresh context window</sub>
-```
-
-## Gap Closure Plans Created
-
-```markdown
-## GAP CLOSURE PLANS CREATED
-
-**Phase:** {phase-name}
-**Closing:** {N} gaps from {VERIFICATION|UAT}.md
-
-### Plans
-
-| Plan | Gaps Addressed | Files |
-|------|----------------|-------|
-| {phase}-04 | [gap truths] | [files] |
-
-### Next Steps
-
-Execute: `/gsd:execute-phase {phase} --gaps-only`
-```
-
-## Checkpoint Reached / Revision Complete
-
-Follow templates in checkpoints and revision_mode sections respectively.
-
-## Chunked Mode Returns
+See @~/.claude/gsd-core/references/planner-guidance.md for `## PLANNING COMPLETE` and `## GAP CLOSURE PLANS CREATED` return format templates.
 
 See @~/.claude/gsd-core/references/planner-chunked.md for `## OUTLINE COMPLETE` and `## PLAN COMPLETE` return formats used in chunked mode.
 
diff --git a/agents/gsd-project-researcher.md b/agents/gsd-project-researcher.md
index 2c79ece7a..0cd91c8a7 100644
--- a/agents/gsd-project-researcher.md
+++ b/agents/gsd-project-researcher.md
@@ -76,7 +76,8 @@ Construct a JSON file at a temp path (e.g. `/tmp/research-plan-input.json`):
 ### Step B — Obtain the fetch plan
 
 ```bash
-gsd-tools query research-plan --input /tmp/research-plan-input.json
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run query research-plan --input /tmp/research-plan-input.json
 ```
 
 Returns `{ "items": [ { "question": "...", "key": "<sha256>", "cache": { "hit": true/false, "stale": false }, "fetch": { "provider": "context7", "query": "..." } } ] }`.
@@ -111,7 +112,7 @@ For any other provider id `X` not listed above: use `mcp__X__*` if available, el
 After digesting a source, persist it so future runs can reuse it:
 
 ```bash
-gsd-tools query research-store put <key> \
+gsd_run query research-store put <key> \
   --content "<one-paragraph digest>" \
   --source <curated|web> \
   --provider <provider-id> \
@@ -128,9 +129,9 @@ gsd-tools query research-store put <key> \
 Obtain the confidence tier from code — do not hard-code tiers in your reasoning:
 
 ```bash
-gsd-tools query classify-confidence --provider <provider-id>
+gsd_run query classify-confidence --provider <provider-id>
 # for cross-checked findings, add --verified:
-gsd-tools query classify-confidence --provider <provider-id> --verified
+gsd_run query classify-confidence --provider <provider-id> --verified
 ```
 
 Returns `HIGH`, `MEDIUM`, or `LOW`. Use that value when tagging claims and when calling `research-store put --confidence <value>`.
diff --git a/agents/gsd-research-synthesizer.md b/agents/gsd-research-synthesizer.md
index 561b76126..c2e8aaba8 100644
--- a/agents/gsd-research-synthesizer.md
+++ b/agents/gsd-research-synthesizer.md
@@ -151,7 +151,8 @@ Write to `.planning/research/SUMMARY.md`.
 The 4 parallel researcher agents write files but do NOT commit. You commit everything together.
 
 ```bash
-gsd-tools query commit "docs: complete project research" --files .planning/research/
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run query commit "docs: complete project research" --files .planning/research/
 ```
 
 ## Step 8: Return Summary
diff --git a/agents/gsd-ui-researcher.md b/agents/gsd-ui-researcher.md
index 63a7d6f84..22157c0d4 100644
--- a/agents/gsd-ui-researcher.md
+++ b/agents/gsd-ui-researcher.md
@@ -286,7 +286,8 @@ This file is the canonical output of this agent. The orchestrator reads `$PHASE_
 ## Step 6: Commit (optional)
 
 ```bash
-gsd-tools query commit "docs($PHASE): UI design contract" --files "$PHASE_DIR/$PADDED_PHASE-UI-SPEC.md"
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
+gsd_run query commit "docs($PHASE): UI design contract" --files "$PHASE_DIR/$PADDED_PHASE-UI-SPEC.md"
 ```
 
 ## Step 7: Return Structured Result
diff --git a/agents/gsd-verifier.md b/agents/gsd-verifier.md
index 3bb38db9d..65736587e 100644
--- a/agents/gsd-verifier.md
+++ b/agents/gsd-verifier.md
@@ -99,9 +99,10 @@ Set `is_re_verification = false`, proceed with Step 1.
 ## Step 1: Load Context (Initial Mode Only)
 
 ```bash
+_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="$HOME/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi
 ls "$PHASE_DIR"/*-PLAN.md 2>/dev/null
 ls "$PHASE_DIR"/*-SUMMARY.md 2>/dev/null
-gsd-tools query roadmap.get-phase "$PHASE_NUM"
+gsd_run query roadmap.get-phase "$PHASE_NUM"
 grep -E "^| $PHASE_NUM" .planning/REQUIREMENTS.md 2>/dev/null
 ```
 
@@ -114,7 +115,7 @@ In re-verification mode, must-haves come from Step 0.
 **Step 2a: Always load ROADMAP Success Criteria**
 
 ```bash
-PHASE_DATA=$(gsd-tools query roadmap.get-phase "$PHASE_NUM" --raw)
+PHASE_DATA=$(gsd_run query roadmap.get-phase "$PHASE_NUM" --raw)
 ```
 
 Parse the `success_criteria` array from the JSON output. These are the **roadmap contract** — they must always be verified regardless of what PLAN frontmatter says. Store them as `roadmap_truths`.
@@ -219,7 +220,7 @@ overrides:
 Use `gsd-tools query` for artifact verification against must_haves in PLAN frontmatter:
 
 ```bash
-ARTIFACT_RESULT=$(gsd-tools query verify.artifacts "$PLAN_PATH")
+ARTIFACT_RESULT=$(gsd_run query verify.artifacts "$PLAN_PATH")
 ```
 
 Parse JSON result: `{ all_passed, passed, total, artifacts: [{path, exists, issues, passed}] }`
@@ -325,7 +326,7 @@ Key links are critical connections. If broken, the goal fails even with all arti
 Use `gsd-tools query` for key link verification against must_haves in PLAN frontmatter:
 
 ```bash
-LINKS_RESULT=$(gsd-tools query verify.key-links "$PLAN_PATH")
+LINKS_RESULT=$(gsd_run query verify.key-links "$PLAN_PATH")
 ```
 
 Parse JSON result: `{ all_verified, verified, total, links: [{from, to, via, verified, detail}] }`
@@ -407,12 +408,12 @@ Identify files modified in this phase from SUMMARY.md key-files section, or extr
 
 ```bash
 # Option 1: Extract from SUMMARY frontmatter
-SUMMARY_FILES=$(gsd-tools query summary-extract "$PHASE_DIR"/*-SUMMARY.md --fields key-files)
+SUMMARY_FILES=$(gsd_run query summary-extract "$PHASE_DIR"/*-SUMMARY.md --fields key-files)
 
 # Option 2: Verify commits exist (if commit hashes documented)
 COMMIT_HASHES=$(grep -oE "[a-f0-9]{7,40}" "$PHASE_DIR"/*-SUMMARY.md | head -10)
 if [ -n "$COMMIT_HASHES" ]; then
-  COMMITS_VALID=$(gsd-tools query verify.commits $COMMIT_HASHES)
+  COMMITS_VALID=$(gsd_run query verify.commits $COMMIT_HASHES)
 fi
 
 # Fallback: grep for files
@@ -587,7 +588,7 @@ Before reporting gaps, check if any identified gaps are explicitly addressed in
 **Load the full milestone roadmap:**
 
 ```bash
-ROADMAP_DATA=$(gsd-tools query roadmap.analyze --raw)
+ROADMAP_DATA=$(gsd_run query roadmap.analyze --raw)
 ```
 
 Parse the JSON to extract all phases. Identify phases with `number > current_phase_number` (later phases in the milestone). For each later phase, extract its `goal` and `success_criteria`.
@@ -662,7 +663,7 @@ Deferred items are informational only — they do not require closure plans.
 **User Story format guard:** Apply via the centralized verb instead of inlining the regex:
 
 ```bash
-USER_STORY_VALID=$(gsd-tools query user-story.validate --story "$PHASE_GOAL" --pick valid)
+USER_STORY_VALID=$(gsd_run query user-story.validate --story "$PHASE_GOAL" --pick valid)
 ```
 
 If `valid != true`, refuse to verify. Surface the discrepancy and ask the user to run `/gsd mvp-phase ${PHASE}` to set a proper User Story goal. The verb owns the canonical regex `/^As a .+, I want to .+, so that .+\.$/` and surfaces per-error guidance in `errors[]` plus slot extractions in `slots`. Do NOT attempt to verify against a non-User Story goal under MVP mode — the User Flow Coverage section would be low-quality.
diff --git a/docs/INVENTORY-MANIFEST.json b/docs/INVENTORY-MANIFEST.json
index fee57e5d0..9cf874497 100644
--- a/docs/INVENTORY-MANIFEST.json
+++ b/docs/INVENTORY-MANIFEST.json
@@ -225,6 +225,7 @@
       "planner-chunked.md",
       "planner-gap-closure.md",
       "planner-graphify-auto-update.md",
+      "planner-guidance.md",
       "planner-human-verify-mode.md",
       "planner-interface-context.md",
       "planner-load-graph-context.md",
diff --git a/docs/INVENTORY.md b/docs/INVENTORY.md
index 76c226cf3..85ec0afb1 100644
--- a/docs/INVENTORY.md
+++ b/docs/INVENTORY.md
@@ -264,7 +264,7 @@ Full roster at `gsd-core/workflows/*.md`. Workflows are thin orchestrators that
 
 ---
 
-## References (67 shipped)
+## References (68 shipped)
 
 Full roster at `gsd-core/references/*.md`. References are shared knowledge documents that workflows and agents `@-reference`. The groupings below match [`docs/ARCHITECTURE.md`](ARCHITECTURE.md#references-gsd-corereferencesmd) — core, workflow, thinking-model clusters, and the modular planner decomposition.
 
@@ -354,6 +354,7 @@ The `gsd-planner` agent is decomposed into a core agent plus reference modules t
 | `planner-antipatterns.md` | Planner anti-patterns and specificity examples. |
 | `planner-chunked.md` | Chunked mode return formats (`## OUTLINE COMPLETE`, `## PLAN COMPLETE`) for Windows stdio hang mitigation. |
 | `planner-gap-closure.md` | Gap-closure mode behavior (reads VERIFICATION.md, targeted replanning). |
+| `planner-guidance.md` | Expository planner guidance: philosophy, task types/sizing, interface-first ordering, user setup, dependency graph, granularity calibration, and structured-return templates. |
 | `planner-reviews.md` | Cross-AI review integration (reads REVIEWS.md from `/gsd-review`). |
 | `planner-revision.md` | Plan revision patterns for iterative refinement. |
 | `planner-source-audit.md` | Planner source-audit and authority-limit rules. |
diff --git a/gsd-core/references/planner-guidance.md b/gsd-core/references/planner-guidance.md
new file mode 100644
index 000000000..0ccc7158a
--- /dev/null
+++ b/gsd-core/references/planner-guidance.md
@@ -0,0 +1,186 @@
+# Planner Guidance: Philosophy, Task Calibration, and Output Formats
+
+## Solo Developer + Claude Workflow
+
+Planning for ONE person (the user) and ONE implementer (Claude).
+- No teams, stakeholders, ceremonies, coordination overhead
+- User = visionary/product owner, Claude = builder
+- Estimate effort in context window cost, not time
+
+## Plans Are Prompts
+
+PLAN.md IS the prompt (not a document that becomes one). Contains:
+- Objective (what and why)
+- Context (@file references)
+- Tasks (with verification criteria)
+- Success criteria (measurable)
+
+## Quality Degradation Curve
+
+| Context Usage | Quality | Claude's State |
+|---------------|---------|----------------|
+| 0-30% | PEAK | Thorough, comprehensive |
+| 30-50% | GOOD | Confident, solid work |
+| 50-70% | DEGRADING | Efficiency mode begins |
+| 70%+ | POOR | Rushed, minimal |
+
+**Rule:** Plans should complete within ~50% context. More plans, smaller scope, consistent quality. Each plan: 2-3 tasks max.
+
+## Ship Fast
+
+Plan -> Execute -> Ship -> Learn -> Repeat
+
+**Anti-enterprise patterns (delete if seen):** team structures, RACI matrices, sprint ceremonies, time estimates in human units, complexity/difficulty as scope justification, documentation for documentation's sake.
+
+---
+
+## Task Types
+
+| Type | Use For | Autonomy |
+|------|---------|----------|
+| `auto` | Everything Claude can do independently | Fully autonomous |
+| `checkpoint:human-verify` | Visual/functional verification | Pauses for user |
+| `checkpoint:decision` | Implementation choices | Pauses for user |
+| `checkpoint:human-action` | Truly unavoidable manual steps (rare) | Pauses for user |
+
+**Automation-first rule:** If Claude CAN do it via CLI/API, Claude MUST do it. Checkpoints verify AFTER automation, not replace it.
+
+## Task Sizing
+
+Each task targets **10–30% context consumption**.
+
+| Context Cost | Action |
+|--------------|--------|
+| < 10% context | Too small — combine with a related task |
+| 10-30% context | Right size — proceed |
+| > 30% context | Too large — split into two tasks |
+
+**Context cost signals (use these, not time estimates):**
+- Files modified: 0-3 = ~10-15%, 4-6 = ~20-30%, 7+ = ~40%+ (split)
+- New subsystem: ~25-35%
+- Migration + data transform: ~30-40%
+- Pure config/wiring: ~5-10%
+
+**Too large signals:** Touches >3-5 files, multiple distinct chunks, action section >1 paragraph.
+
+**Combine signals:** One task sets up for the next, separate tasks touch same file, neither meaningful alone.
+
+## Interface-First Task Ordering
+
+When a plan creates new interfaces consumed by subsequent tasks:
+
+1. **First task: Define contracts** — Create type files, interfaces, exports
+2. **Middle tasks: Implement** — Build against the defined contracts
+3. **Last task: Wire** — Connect implementations to consumers
+
+This prevents the "scavenger hunt" anti-pattern where executors explore the codebase to understand contracts. They receive the contracts in the plan itself.
+
+## Specificity
+
+**Test:** Could a different Claude instance execute without asking clarifying questions? If not, add specificity. See @~/.claude/gsd-core/references/planner-antipatterns.md for vague-vs-specific comparison table.
+
+## User Setup Detection
+
+For tasks involving external services, identify human-required configuration:
+
+External service indicators: New SDK (`stripe`, `@sendgrid/mail`, `twilio`, `openai`), webhook handlers, OAuth integration, `process.env.SERVICE_*` patterns.
+
+For each external service, determine:
+1. **Env vars needed** — What secrets from dashboards?
+2. **Account setup** — Does user need to create an account?
+3. **Dashboard config** — What must be configured in external UI?
+
+Record in `user_setup` frontmatter. Only include what Claude literally cannot do. Do NOT surface in planning output — execute-plan handles presentation.
+
+---
+
+## Building the Dependency Graph
+
+**For each task, record:**
+- `needs`: What must exist before this runs
+- `creates`: What this produces
+- `has_checkpoint`: Requires user interaction?
+
+**Example:** A→C, B→D, C+D→E, E→F(checkpoint). Waves: {A,B} → {C,D} → {E} → {F}.
+
+**Prefer vertical slices** (User feature: model+API+UI) over horizontal layers (all models → all APIs → all UIs). Vertical = parallel. Horizontal = sequential. Use horizontal only when shared foundation is required.
+
+## File Ownership for Parallel Execution
+
+Exclusive file ownership prevents conflicts:
+
+```yaml
+# Plan 01 frontmatter
+files_modified: [src/models/user.ts, src/api/users.ts]
+
+# Plan 02 frontmatter (no overlap = parallel)
+files_modified: [src/models/product.ts, src/api/products.ts]
+```
+
+No overlap → can run parallel. File in multiple plans → later plan depends on earlier.
+
+---
+
+## Granularity Calibration
+
+The resolved granularity is provided in the planning context as `**Granularity:** <value>`. Read that value and apply the corresponding row below. When no explicit value is present, default to Standard.
+
+| Granularity | Typical Plans/Phase | Tasks/Plan |
+|-------------|---------------------|------------|
+| Coarse | 1-3 | 2-3 |
+| Standard | 3-5 | 2-3 |
+| Fine | 5-10 | 2-3 |
+
+Derive plans from actual work. Granularity determines compression tolerance, not a target.
+
+---
+
+## Planning Complete Return Format
+
+```markdown
+## PLANNING COMPLETE
+
+**Phase:** {phase-name}
+**Plans:** {N} plan(s) in {M} wave(s)
+
+### Wave Structure
+
+| Wave | Plans | Autonomous |
+|------|-------|------------|
+| 1 | {plan-01}, {plan-02} | yes, yes |
+| 2 | {plan-03} | no (has checkpoint) |
+
+### Plans Created
+
+| Plan | Objective | Tasks | Files |
+|------|-----------|-------|-------|
+| {phase}-01 | [brief] | 2 | [files] |
+| {phase}-02 | [brief] | 3 | [files] |
+
+### Next Steps
+
+Run `/clear` first for a fresh context window, then execute: `/gsd:execute-phase {phase}`
+```
+
+## Gap Closure Plans Created Return Format
+
+```markdown
+## GAP CLOSURE PLANS CREATED
+
+**Phase:** {phase-name}
+**Closing:** {N} gaps from {VERIFICATION|UAT}.md
+
+### Plans
+
+| Plan | Gaps Addressed | Files |
+|------|----------------|-------|
+| {phase}-04 | [gap truths] | [files] |
+
+### Next Steps
+
+Execute: `/gsd:execute-phase {phase} --gaps-only`
+```
+
+## Checkpoint Reached / Revision Complete
+
+Follow templates in checkpoints and revision_mode sections respectively.
diff --git a/scripts/research-profiles.cjs b/scripts/research-profiles.cjs
index 01b0c0e7f..111fd317e 100644
--- a/scripts/research-profiles.cjs
+++ b/scripts/research-profiles.cjs
@@ -13,7 +13,7 @@
  *   color            — verbatim frontmatter `color:` value
  *   tools            — verbatim frontmatter `tools:` value (single string, comma-separated)
  *   requiredIncludes — @~/.claude/gsd-core/references/<file>.md strings the body MUST contain
- *   requiredSeamCalls — `gsd-tools query <cmd>` strings the body MUST contain
+ *   requiredSeamCalls — `gsd_run query <cmd>` strings the body MUST contain
  *   outputContract   — strings the body MUST contain (output path, return marker, etc.)
  */
 
@@ -31,9 +31,9 @@ const PROFILES = [
       '@~/.claude/gsd-core/references/research-verification-protocol.md',
     ],
     requiredSeamCalls: [
-      'gsd-tools query research-plan',
-      'gsd-tools query research-store put',
-      'gsd-tools query classify-confidence',
+      'gsd_run query research-plan',
+      'gsd_run query research-store put',
+      'gsd_run query classify-confidence',
     ],
     outputContract: [
       '.planning/research/',
@@ -53,10 +53,10 @@ const PROFILES = [
       '@~/.claude/gsd-core/references/research-verification-protocol.md',
     ],
     requiredSeamCalls: [
-      'gsd-tools query research-plan',
-      'gsd-tools query research-store put',
-      'gsd-tools query classify-confidence',
-      'gsd-tools query package-legitimacy check',
+      'gsd_run query research-plan',
+      'gsd_run query research-store put',
+      'gsd_run query classify-confidence',
+      'gsd_run query package-legitimacy check',
     ],
     outputContract: [
       '.planning/phases/XX-name/{phase_num}-RESEARCH.md',
@@ -122,7 +122,7 @@ const PROFILES = [
       '@~/.claude/gsd-core/references/research-documentation-lookup.md',
     ],
     requiredSeamCalls: [
-      'gsd-tools query commit',
+      'gsd_run query commit',
     ],
     outputContract: [
       'UI-SPEC.md',
@@ -137,7 +137,7 @@ const PROFILES = [
     tools: 'Read, Write, Bash',
     requiredIncludes: [],
     requiredSeamCalls: [
-      'gsd-tools query commit',
+      'gsd_run query commit',
     ],
     outputContract: [
       '.planning/research/SUMMARY.md',
diff --git a/scripts/sync-runtime-launcher.cjs b/scripts/sync-runtime-launcher.cjs
index fc52ceec4..6ce5a6303 100644
--- a/scripts/sync-runtime-launcher.cjs
+++ b/scripts/sync-runtime-launcher.cjs
@@ -2,8 +2,8 @@
 /**
  * sync-runtime-launcher.cjs
  *
- * Idempotent transform: for every gsd-core/workflows/*.md (and subdirs),
- * rewrite all bash/sh/shell fenced blocks to:
+ * Idempotent transform: for every gsd-core/workflows/*.md (and subdirs)
+ * AND every agents/*.md, rewrite all bash/sh/shell fenced blocks to:
  *   1. Strip ALL old resolver forms from every bash block (GSD_TOOLS=,
  *      GSD_SDK=, the if/elif/else/fi resolver, _GSD_SHIM_NAME=, and any
  *      previously-inserted gsd_run preamble).
@@ -20,6 +20,7 @@ const fs = require('node:fs');
 const path = require('node:path');
 
 const WORKFLOWS_DIR = path.join(__dirname, '..', 'gsd-core', 'workflows');
+const AGENTS_DIR = path.join(__dirname, '..', 'agents');
 const SNIPPET_FILE = path.join(WORKFLOWS_DIR, '_runtime-launcher.snippet.sh');
 
 // Read canonical preamble (full content of snippet file)
@@ -376,18 +377,33 @@ function escapeRegExp(str) {
 // Main
 function main() {
   const preamble = loadPreamble();
-  const files = collectFiles(WORKFLOWS_DIR);
 
   let transformedCount = 0;
   let unchangedCount = 0;
 
-  for (const f of files) {
+  // Process workflow files
+  const workflowFiles = collectFiles(WORKFLOWS_DIR);
+  for (const f of workflowFiles) {
     const content = fs.readFileSync(f, 'utf8');
     const result = transformFile(content, preamble);
     if (result !== null) {
       fs.writeFileSync(f, result, 'utf8');
       transformedCount++;
-      console.log(`transformed: ${path.relative(WORKFLOWS_DIR, f)}`);
+      console.log(`transformed (workflow): ${path.relative(WORKFLOWS_DIR, f)}`);
+    } else {
+      unchangedCount++;
+    }
+  }
+
+  // Process agent files
+  const agentFiles = collectFiles(AGENTS_DIR);
+  for (const f of agentFiles) {
+    const content = fs.readFileSync(f, 'utf8');
+    const result = transformFile(content, preamble);
+    if (result !== null) {
+      fs.writeFileSync(f, result, 'utf8');
+      transformedCount++;
+      console.log(`transformed (agent): ${path.relative(AGENTS_DIR, f)}`);
     } else {
       unchangedCount++;
     }
diff --git a/tests/bug-2851-workflow-bare-gsd-tools.test.cjs b/tests/bug-2851-workflow-bare-gsd-tools.test.cjs
index d75ad980f..933b5335a 100644
--- a/tests/bug-2851-workflow-bare-gsd-tools.test.cjs
+++ b/tests/bug-2851-workflow-bare-gsd-tools.test.cjs
@@ -119,6 +119,37 @@ function lineHasBareGsdTools(line) {
   return false;
 }
 
+const AGENTS_DIR = path.join(__dirname, '..', 'agents');
+
+describe('bug #1041: agent files must not call bare gsd-tools (all-runtime resolver)', () => {
+  test('no agents/gsd-*.md file contains a bare gsd-tools command', () => {
+    const files = fs.readdirSync(AGENTS_DIR).filter((f) => f.startsWith('gsd-') && f.endsWith('.md'));
+    assert.ok(files.length > 0, 'expected agent files to exist');
+
+    const violations = [];
+    for (const f of files) {
+      const full = path.join(AGENTS_DIR, f);
+      const content = fs.readFileSync(full, 'utf-8');
+      const blocks = extractShellBlocks(content);
+      for (const blk of blocks) {
+        for (let i = 0; i < blk.lines.length; i++) {
+          if (lineHasBareGsdTools(blk.lines[i])) {
+            violations.push(`${f}:${blk.startLine + i}: ${blk.lines[i].trim()}`);
+          }
+        }
+      }
+    }
+
+    assert.deepStrictEqual(
+      violations,
+      [],
+      'Bare `gsd-tools` invocations found in agent shell blocks. ' +
+        'Inject the runtime-launcher preamble (_runtime-launcher.snippet.sh) and use `gsd_run` instead.\n' +
+        violations.join('\n'),
+    );
+  });
+});
+
 describe('bug-2851: workflow files must not call bare `gsd-tools` (#2245 sweep regression)', () => {
   test('no gsd-core/workflows/*.md file contains a bare gsd-tools command', () => {
     const files = fs.readdirSync(WORKFLOWS_DIR).filter((f) => f.endsWith('.md'));
diff --git a/tests/runtime-launcher-parity.test.cjs b/tests/runtime-launcher-parity.test.cjs
index 1dd5efd85..690b98b18 100644
--- a/tests/runtime-launcher-parity.test.cjs
+++ b/tests/runtime-launcher-parity.test.cjs
@@ -32,6 +32,7 @@ const { execFileSync } = require('node:child_process');
 const { cleanup } = require('./helpers.cjs');
 
 const WORKFLOWS_DIR = path.join(__dirname, '..', 'gsd-core', 'workflows');
+const AGENTS_DIR = path.join(__dirname, '..', 'agents');
 const SNIPPET_FILE = path.join(WORKFLOWS_DIR, '_runtime-launcher.snippet.sh');
 
 /**
@@ -115,6 +116,26 @@ function collectWorkflowFiles() {
   return results;
 }
 
+/**
+ * Collect all agent .md files under AGENTS_DIR (non-recursive — agents/ has no subdirs,
+ * but collectFiles in the sync script is recursive-safe; we mirror that here).
+ */
+function collectAgentFiles() {
+  const results = [];
+  function walk(dir) {
+    for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+      const full = path.join(dir, entry.name);
+      if (entry.isDirectory()) {
+        walk(full);
+      } else if (entry.isFile() && entry.name.endsWith('.md')) {
+        results.push(full);
+      }
+    }
+  }
+  walk(AGENTS_DIR);
+  return results;
+}
+
 describe('runtime-launcher-parity (#373)', () => {
   // ─── (A) No retired GSD_SDK token ────────────────────────────────────────
   test('(A) no GSD_SDK token in any workflow .md file', () => {
@@ -524,3 +545,70 @@ describe('runtime-launcher-parity (#373)', () => {
     );
   });
 });
+
+// ─── Agent parity — runtime-launcher-parity — agents (#1041) ─────────────────
+describe('runtime-launcher-parity — agents (#1041)', () => {
+  // ─── (B-agents) Exactly ONE canonical preamble per using agent file ────────
+  test('(B-agents) each agent .md using gsd_run contains exactly ONE canonical preamble, before the first gsd_run call', () => {
+    const preamble = expectedPreamble();
+    const preambleStr = preamble.join('\n');
+    const files = collectAgentFiles();
+    assert.ok(files.length > 0, 'expected at least one agent .md file');
+
+    const violations = [];
+
+    for (const f of files) {
+      const rel = path.relative(AGENTS_DIR, f);
+      const content = fs.readFileSync(f, 'utf8');
+      const blocks = extractShellBlocks(content);
+
+      // Collect all block lines in document order for flat analysis
+      const allBlockLines = [];
+      for (const blk of blocks) {
+        allBlockLines.push(...blk.lines);
+      }
+
+      // Does this file use gsd_run at all?
+      const fileHasGsdRun = allBlockLines.some((l) => /\bgsd_run\b/.test(l));
+      if (!fileHasGsdRun) continue; // agents without gsd_run are not checked
+
+      // Count preamble occurrences across all shell content of this file
+      const allContent = allBlockLines.join('\n');
+      let preambleCount = 0;
+      let searchPos = 0;
+      while (true) {
+        const idx = allContent.indexOf(preambleStr, searchPos);
+        if (idx === -1) break;
+        preambleCount++;
+        searchPos = idx + preambleStr.length;
+      }
+
+      if (preambleCount !== 1) {
+        violations.push(
+          `${rel}: expected exactly 1 canonical preamble occurrence in bash blocks, found ${preambleCount}. ` +
+            `Run \`node scripts/sync-runtime-launcher.cjs\` to fix.`,
+        );
+        continue;
+      }
+
+      // Verify preamble appears BEFORE the first gsd_run call (in document order)
+      const preamblePos = allContent.indexOf(preambleStr);
+      const firstGsdRunPos = allContent.search(/\bgsd_run\b/);
+
+      // The first gsd_run WITHIN the preamble itself (the function definition) is fine.
+      // Simple check: preamble starts at or before the first gsd_run occurrence.
+      if (preamblePos > firstGsdRunPos) {
+        violations.push(
+          `${rel}: preamble appears AFTER the first gsd_run reference — it must precede all gsd_run calls.`,
+        );
+      }
+    }
+
+    assert.deepStrictEqual(
+      violations,
+      [],
+      'Agent files with gsd_run calls have wrong preamble count or ordering:\n' +
+        violations.join('\n---\n'),
+    );
+  });
+});