diff --git a/agents/gsd-executor.md b/agents/gsd-executor.md
index 55c4f14c5..e5989f648 100644
--- a/agents/gsd-executor.md
+++ b/agents/gsd-executor.md
@@ -205,13 +205,14 @@ Do NOT continue reading. Analysis without action is a stuck signal.
 </authentication_gates>
 
 <auto_mode_detection>
-Check if auto mode is active at executor start:
+Check if auto mode is active at executor start (chain flag or user preference):
 
 ```bash
+AUTO_CHAIN=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow._auto_chain_active 2>/dev/null || echo "false")
 AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
 ```
 
-Store the result for checkpoint handling below.
+Auto mode is active if either `AUTO_CHAIN` or `AUTO_CFG` is `"true"`. Store the result for checkpoint handling below.
 </auto_mode_detection>
 
 <checkpoint_protocol>
diff --git a/get-shit-done/references/checkpoints.md b/get-shit-done/references/checkpoints.md
index 04db7ade2..232817480 100644
--- a/get-shit-done/references/checkpoints.md
+++ b/get-shit-done/references/checkpoints.md
@@ -8,7 +8,7 @@ Plans execute autonomously. Checkpoints formalize interaction points where human
 2. **Claude sets up the verification environment** - Start dev servers, seed databases, configure env vars
 3. **User only does what requires human judgment** - Visual checks, UX evaluation, "does this feel right?"
 4. **Secrets come from user, automation comes from Claude** - Ask for API keys, then Claude uses them via CLI
-5. **Auto-mode bypasses verification/decision checkpoints** — When `workflow.auto_advance` is true in config: human-verify auto-approves, decision auto-selects first option, human-action still stops (auth gates cannot be automated)
+5. **Auto-mode bypasses verification/decision checkpoints** — When `workflow._auto_chain_active` or `workflow.auto_advance` is true in config: human-verify auto-approves, decision auto-selects first option, human-action still stops (auth gates cannot be automated)
 </overview>
 
 <checkpoint_types>
diff --git a/get-shit-done/workflows/discuss-phase.md b/get-shit-done/workflows/discuss-phase.md
index d5fb5a67c..a82f36768 100644
--- a/get-shit-done/workflows/discuss-phase.md
+++ b/get-shit-done/workflows/discuss-phase.md
@@ -589,17 +589,24 @@ node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs(state): record
 Check for auto-advance trigger:
 
 1. Parse `--auto` flag from $ARGUMENTS
-2. Read `workflow.auto_advance` from config:
+2. **Sync chain flag with intent** — if user invoked manually (no `--auto`), clear the ephemeral chain flag from any previous interrupted `--auto` chain. This does NOT touch `workflow.auto_advance` (the user's persistent settings preference):
    ```bash
+   if [[ ! "$ARGUMENTS" =~ --auto ]]; then
+     node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active false 2>/dev/null
+   fi
+   ```
+3. Read both the chain flag and user preference:
+   ```bash
+   AUTO_CHAIN=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow._auto_chain_active 2>/dev/null || echo "false")
    AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
    ```
 
-**If `--auto` flag present AND `AUTO_CFG` is not true:** Persist auto-advance to config (handles direct `--auto` usage without new-project):
+**If `--auto` flag present AND `AUTO_CHAIN` is not true:** Persist chain flag to config (handles direct `--auto` usage without new-project):
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow.auto_advance true
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active true
 ```
 
-**If `--auto` flag present OR `AUTO_CFG` is true:**
+**If `--auto` flag present OR `AUTO_CHAIN` is true OR `AUTO_CFG` is true:**
 
 Display banner:
 ```
diff --git a/get-shit-done/workflows/execute-phase.md b/get-shit-done/workflows/execute-phase.md
index 5149594ce..8d37e5994 100644
--- a/get-shit-done/workflows/execute-phase.md
+++ b/get-shit-done/workflows/execute-phase.md
@@ -26,6 +26,13 @@ Parse JSON for: `executor_model`, `verifier_model`, `commit_docs`, `parallelizat
 **If `state_exists` is false but `.planning/` exists:** Offer reconstruct or continue.
 
 When `parallelization` is false, plans within a wave execute sequentially.
+
+**Sync chain flag with intent** — if user invoked manually (no `--auto`), clear the ephemeral chain flag from any previous interrupted `--auto` chain. This does NOT touch `workflow.auto_advance` (the user's persistent settings preference). Must happen before any config reads (checkpoint handling also reads auto-advance flags):
+```bash
+if [[ ! "$ARGUMENTS" =~ --auto ]]; then
+  node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active false 2>/dev/null
+fi
+```
 </step>
 
 <step name="handle_branching">
@@ -179,12 +186,13 @@ Plans with `autonomous: false` require user interaction.
 
 **Auto-mode checkpoint handling:**
 
-Read auto-advance config:
+Read auto-advance config (chain flag + user preference):
 ```bash
+AUTO_CHAIN=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow._auto_chain_active 2>/dev/null || echo "false")
 AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
 ```
 
-When executor returns a checkpoint AND `AUTO_CFG` is `"true"`:
+When executor returns a checkpoint AND (`AUTO_CHAIN` is `"true"` OR `AUTO_CFG` is `"true"`):
 - **human-verify** → Auto-spawn continuation agent with `{user_response}` = `"approved"`. Log `⚡ Auto-approved checkpoint`.
 - **decision** → Auto-spawn continuation agent with `{user_response}` = first option from checkpoint details. Log `⚡ Auto-selected: [option]`.
 - **human-action** → Present to user (existing behavior below). Auth gates cannot be automated.
@@ -405,12 +413,13 @@ STOP. Do not proceed to auto-advance or transition.
 **Auto-advance detection:**
 
 1. Parse `--auto` flag from $ARGUMENTS
-2. Read `workflow.auto_advance` from config:
+2. Read both the chain flag and user preference (chain flag already synced in init step):
    ```bash
+   AUTO_CHAIN=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow._auto_chain_active 2>/dev/null || echo "false")
    AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
    ```
 
-**If `--auto` flag present OR `AUTO_CFG` is true (AND verification passed with no gaps):**
+**If `--auto` flag present OR `AUTO_CHAIN` is true OR `AUTO_CFG` is true (AND verification passed with no gaps):**
 
 ```
 ╔══════════════════════════════════════════╗
diff --git a/get-shit-done/workflows/new-project.md b/get-shit-done/workflows/new-project.md
index c2d2e2ba8..0ccd254a9 100644
--- a/get-shit-done/workflows/new-project.md
+++ b/get-shit-done/workflows/new-project.md
@@ -191,10 +191,10 @@ mkdir -p .planning
 node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "chore: add project config" --files .planning/config.json
 ```
 
-**Persist auto-advance to config (survives context compaction):**
+**Persist auto-advance chain flag to config (survives context compaction):**
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow.auto_advance true
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active true
 ```
 
 Proceed to Step 4 (skip Steps 3 and 5).
diff --git a/get-shit-done/workflows/plan-phase.md b/get-shit-done/workflows/plan-phase.md
index 4ac899b7e..bfa8d136c 100644
--- a/get-shit-done/workflows/plan-phase.md
+++ b/get-shit-done/workflows/plan-phase.md
@@ -441,12 +441,19 @@ Route to `<offer_next>` OR `auto_advance` depending on flags/config.
 Check for auto-advance trigger:
 
 1. Parse `--auto` flag from $ARGUMENTS
-2. Read `workflow.auto_advance` from config:
+2. **Sync chain flag with intent** — if user invoked manually (no `--auto`), clear the ephemeral chain flag from any previous interrupted `--auto` chain. This does NOT touch `workflow.auto_advance` (the user's persistent settings preference):
    ```bash
+   if [[ ! "$ARGUMENTS" =~ --auto ]]; then
+     node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active false 2>/dev/null
+   fi
+   ```
+3. Read both the chain flag and user preference:
+   ```bash
+   AUTO_CHAIN=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow._auto_chain_active 2>/dev/null || echo "false")
    AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
    ```
 
-**If `--auto` flag present OR `AUTO_CFG` is true:**
+**If `--auto` flag present OR `AUTO_CHAIN` is true OR `AUTO_CFG` is true:**
 
 Display banner:
 ```
diff --git a/get-shit-done/workflows/transition.md b/get-shit-done/workflows/transition.md
index 553fc193b..5e8927dfd 100644
--- a/get-shit-done/workflows/transition.md
+++ b/get-shit-done/workflows/transition.md
@@ -451,9 +451,9 @@ Exit skill and invoke SlashCommand("/gsd:discuss-phase [X+1] --auto")
 
 **Route B: Milestone complete (all phases done)**
 
-**Clear auto-advance** — milestone boundary is the natural stopping point:
+**Clear auto-advance chain flag** — milestone boundary is the natural stopping point:
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow.auto_advance false
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-set workflow._auto_chain_active false
 ```
 
 <if mode="yolo">