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/references/planning-config.md

@@ -34,7 +34,7 @@ Configuration options for `.planning/` directory behavior.
 | `git.phase_branch_template` | `"gsd/phase-{phase}-{slug}"` | Branch template for phase strategy |
 | `git.milestone_branch_template` | `"gsd/{milestone}-{slug}"` | Branch template for milestone strategy |
 | `git.quick_branch_template` | `null` | Optional branch template for quick-task runs |
-| `workflow.use_worktrees` | `true` | Whether executor agents run in isolated git worktrees. Set to `false` to disable worktrees — agents execute sequentially on the main working tree instead. Recommended for solo developers or when worktree merges cause issues. |
+| `workflow.use_worktrees` | `true` | Whether executor agents run in isolated git worktrees. Set to `false` to disable worktrees — agents execute sequentially on the main working tree instead. Recommended for solo developers or when worktree merges cause issues. Note: if your branch is ahead of `origin/HEAD` (a diverged milestone or feature branch), GSD auto-degrades to sequential and prints a warning; set `worktree.baseRef:"head"` in `.claude/settings.local.json` to restore parallel execution. See the branch-divergence note below. |
 | `workflow.subagent_timeout` | `300000` | Timeout in milliseconds for parallel subagent tasks (e.g. codebase mapping). Increase for large codebases or slower models. Default: 300000 (5 minutes). |
 | `workflow.inline_plan_threshold` | `2` | Plans with this many tasks or fewer execute inline (Pattern C) instead of spawning a subagent. Avoids ~14K token spawn overhead for small plans. Set to `0` to always spawn subagents. |
 | `manager.flags.discuss` | `""` | Flags passed to `/gsd:discuss-phase` when dispatched from manager (e.g. `"--auto --analyze"`) |
@@ -385,6 +385,8 @@ Several config fields affect each other or trigger special behavior:
 
 8. **`sub_repos` auto-sync** -- On every config load, GSD scans for child directories with `.git` and updates the `sub_repos` array if the filesystem has changed. Legacy `multiRepo: true` is automatically migrated to a detected `sub_repos` array.
 
+9. **`workflow.use_worktrees` and branch divergence** -- When `use_worktrees` is `true` (default), executor worktrees are forked from `origin/HEAD` by the Claude Code harness. If your current branch has commits that `origin/HEAD` does not (for example an unmerged milestone or feature branch), GSD automatically degrades to sequential execution for that run and prints a one-line `⚠ Worktree base mismatch` warning. To restore parallel execution permanently, set `worktree.baseRef:"head"` in `.claude/settings.local.json` (run `node gsd-tools.cjs worktree set-baseref`). This makes the harness fork worktrees from the live HEAD instead of `origin/HEAD`. Both fresh installs and upgrades of GSD Core set this automatically (no-clobber) when `use_worktrees` is enabled; you can also run the command manually at any time. Setting `workflow.use_worktrees: false` is the alternative if worktrees are not needed at all.
+
 ---
 
 ## Example Configurations