fix(#683): auto-degrade phase execution to sequential on worktree base mismatch (#749)

* fix(#683): auto-degrade phase execution to sequential on worktree base mismatch

Claude Code forks worktree-isolated executors off the repository default
branch (origin/HEAD), not the orchestrator's HEAD. Running /gsd-execute-phase
on a branch diverged from the default (unmerged milestone/feature branch) left
every executor without the phase's plan files and tripped the
worktree-branch-check guard with `exit 42` — 100% reproducible, all OSes.

- New module src/worktree-base-ref.cts: HEAD-vs-fork-base drift detection
  (origin/HEAD with symbolic-ref fallback) and no-clobber worktree.baseRef
  management, exposed as `worktree base-check` / `worktree set-baseref`.
- execute-phase.md: pre-dispatch, for Claude Code with worktrees enabled,
  auto-degrades the run to sequential on the main tree when a base mismatch
  is detected, recommending worktree.baseRef:"head". The exit-42 guard stays
  as a backstop.
- Installer: fresh local Claude installs set worktree.baseRef:"head" in
  .claude/settings.local.json (no-clobber, respecting an explicit shared
  settings.json value); upgrades print an opt-in notice pointing at
  `gsd-tools worktree set-baseref`.
- Docs: how-to guide, CLI/config reference, planning-config cross-ref.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(#683): auto-apply worktree.baseRef on upgrade; gate fresh+upgrade on use_worktrees

Per maintainer direction: on a local Claude Code UPGRADE, set
worktree.baseRef:"head" automatically (no opt-in notice) when the project's
workflow.use_worktrees is enabled, instead of merely printing a remediation
notice. For consistency the FRESH path is now gated the same way: both paths
compute worktrees-enabled once (bounded walk-up read of .planning/config.json,
default enabled unless workflow.use_worktrees === false) and apply the
no-clobber baseRef only when enabled — never overwriting an explicit value in
settings.local.json or a shared settings.json. gsd-tools worktree set-baseref
remains for manual use. Docs + changeset updated; tests hardened (file-exists
assertions, fresh+disabled case, upgrade idempotency).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(#683): measure workflow byte-budget on LF, fixing Windows-only CI failure

The workflow-size-budget test failed only on Windows: git checks out the .md
files as CRLF (no eol=lf in .gitattributes) and byteCount used
fs.statSync().size (raw on-disk bytes), counting an extra \r per line. That
inflated execute-phase.md — the XL high-water-mark file pinned near its ceiling
by the tighten-only ratchet — from 88492 LF bytes to ~90245 on Windows, over
the 90000 XL ceiling, while passing on the LF-checkout Mac/Linux runners.

The ceilings are explicitly "calibrated against raw `wc -c`" on an LF checkout,
so the measurement should be LF-based on every platform. byteCount now reads the
file and counts Buffer.byteLength after stripping CR, making the budget
platform-independent (a no-op on LF checkouts; verified statSync === normalized
for all 88 workflow files). No ceilings changed. Added a regression test
asserting CRLF and LF content of the same file count identically.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(#683): make worktree-base-ref test path mocks Windows-safe (path.join)

tests/worktree-base-ref.test.cjs keyed its injected readFile/writeFile mocks
(and a few expected `file` values) with forward-slash template literals like
`${claudeDir}/settings.local.json`. The module composes those paths with
path.join(), which emits backslashes on Windows, so the mock keys never matched
the module's lookup → readFile returned null → resolveEffectiveBaseRef /
cmdWorktreeBaseCheck / cmdWorktreeSetBaseRef (and the JSONC variants) failed on
the Windows full-test runner only (they passed on Mac/Linux, and the install
tests passed because they use the real filesystem). The module is correct;
only the test fixtures hardcoded '/'.

All mock keys and path assertions now use path.join(base, ...) mirroring the
module, so they match on every platform (no-op on POSIX). 19 path references
across 16 lines.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

gsd-core/workflows/execute-phase.md

@@ -92,6 +92,16 @@ if [ "$RUNTIME" = "codex" ] && [ "$USE_WORKTREES" != "false" ]; then
 fi
 # Sweep orphaned locked worktrees from prior crashed sessions before spawning executors (#3707).
 [ "$USE_WORKTREES" != "false" ] && gsd_run query worktree.reap-orphans 2>/dev/null || true
+# Auto-degrade to sequential if HEAD has diverged from the worktree fork base (#683).
+# Only applies to Claude Code (isolation="worktree" is Claude-Code-specific).
+if [ "$RUNTIME" = "claude" ] && [ "$USE_WORKTREES" != "false" ]; then
+  _SHOULD_DEGRADE=$(gsd_run query worktree.base-check --pick shouldDegrade 2>/dev/null || true)
+  if [ "$_SHOULD_DEGRADE" = "true" ]; then
+    _DEGRADE_MSG=$(gsd_run query worktree.base-check --pick message 2>/dev/null || true)
+    [ -n "$_DEGRADE_MSG" ] && printf '%s\n' "$_DEGRADE_MSG" >&2
+    USE_WORKTREES=false
+  fi
+fi
 ```
 Codex maps subagents to `spawn_agent`, which has no direct Codex mapping for Claude Code's `isolation="worktree"` parameter. Failing closed prevents main-checkout edits while the workflow believes agents are isolated.
 
@@ -111,6 +121,8 @@ fi
 
 When `USE_WORKTREES` (project-level) is `false`, all executor agents run without `isolation="worktree"` — they execute sequentially on the main working tree instead of in parallel worktrees. The per-plan decision below has no effect when worktrees are project-disabled.
 
+`USE_WORKTREES` is also automatically set to `false` for the duration of a run when `worktree base-check` detects that the orchestrator HEAD has diverged from the worktree fork base (the #683 condition — e.g. an unmerged milestone or feature branch). This check runs only when `RUNTIME=claude` because `isolation="worktree"` is a Claude Code-specific feature; other runtimes do not use it. The auto-degrade prints a one-line warning to stderr and falls through to the sequential path so executors do not hit the exit-42 worktree-branch-check halt. To restore parallel worktree execution, set `worktree.baseRef:"head"` in `.claude/settings.local.json` (or run `gsd-tools worktree set-baseref`) — this makes the fork base track the live HEAD instead of a fixed remote ref. The `worktree-branch-check` exit-42 guard inside each executor remains in place as a backstop.
+
 Read context window size for adaptive prompt enrichment:
 
 ```bash