fix(#4619): execute-phase computes decimal/N-segment phase numbers without breaking shell arithmetic (#4644)

* fix(#4619): execute-phase computes decimal/N-segment phase numbers without breaking shell arithmetic

$((10#${PHASE_NUMBER})) is a hard bash/zsh syntax error when PHASE_NUMBER is
decimal (01.1, from an inserted phase) or N-segment (23.1.2) — neither is
valid shell-arithmetic syntax at all, and the failed expansion aborts the
rest of the snippet in a non-interactive shell. safe_resume_gate runs
unconditionally before trusting STATE.md or dispatching any executor, so
execute-phase failed at its own gate before the first executor on any
decimal phase, regardless of workflow.tdd_mode. Regression from #4194.

Fixes all 4 sites: safe_resume_gate and the TDD gate in
workflows/execute-phase.md, the completion-signal spot-check fallback in
workflows/execute-phase/steps/completion-reconciliation.md, and the
executor gate validation example in references/tdd.md. Each now zero-strips
only the leading integer segment into a *_INT variable (via %%.* / #
parameter expansion — always valid shell syntax regardless of what follows)
and keeps the remainder as an escaped-dot string for the anchored commit-
scope regex, exactly as issue #4619 verified in both bash and zsh. A plain
integer phase (12, 01) computes byte-identically to before.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* test(#4619): pin the decimal/N-segment fix and characterize the pre-fix bug

Behavioral coverage via real bash execution: the old $((10#01.1)) form
throws (characterizes the bug, matching the issue's own reproduction); the
new form resolves 01.1 -> 1\.1 and 23.1.2 -> 23\.1\.2, unchanged for plain
integers (12 -> 12, 01 -> 1); the resulting anchored ERE matches
feat(01.1-03):/test(1.1-3): and correctly rejects feat(01-03):,
feat(01.2-03):, feat(011-03):, feat(12-03): for a decimal phase — mirroring
issue #4619's own verified table exactly. Updates
safe-resume-gate-anchoring.test.cjs's 4 existing source-text assertions
(one per site) to the new fixed text.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* chore(#4634): refine the shell-arith drift detector to distinguish safe from unsafe arithmetic

With #4619's fix in place, the guard's original "ban $((10#... outright,
match any occurrence" was too blunt: it flagged a comment merely mentioning
the pattern in prose, the now-safe $((10#$PHASE_INT)) arithmetic on an
already-%%.*-stripped integer, and the always-safe plan-id arithmetic
(plan ids are plain integers, never decimal). Refines the detector to skip
full-line comments and to only flag a captured variable/placeholder name
that contains "phase" and does NOT end in _INT/_int — the naming convention
the #4619 fix establishes at all four sites for "already reduced to a safe
integer." A plan-id variable was never phase-number arithmetic in the first
place and is excluded on the same basis.

This closes epic #4634's D6 ("lint-phase-id-drift... passes with no new
exemptions") and D7 ("a decimal and N-segment phase id survive an
end-to-end execute-phase selection without error") for real — the guard now
reports zero violations across all five .cts/.md rules.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* chore: regenerate conformance-tier manifests for the new test file

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* test(#4619): cover the plain-padded-integer near-miss matrix too

Review found the anchored-ERE near-miss coverage only exercised the
decimal case (PHASE_NUMBER=01.1); issue #4619's own worked table also
verifies the plain padded-integer case (01 -> PHASE_N=1) against its own
near-miss set (matches 01-03, rejects 01.1-03/011-03/12-03). Adds the
missing assertion.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* docs(#4619): add Fixed changeset

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(#4619): correct JS backslash-escaping in safe-resume-gate anchoring test

The test's string-literal assertions for the PHASE_FRAC//./\\.} pattern wrote
only 2 backslash characters in JS source, which single-quoted-string parsing
collapses to 1 real backslash at runtime -- but the workflow/reference files
actually contain 2 raw backslash bytes at that position (needed so bash's
${var//pattern/replacement} produces the correct single-backslash output).
Write 4 backslash characters in the JS source at all 4 occurrences so the
runtime string matches the files' real bytes.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* chore(#4619): refresh the committed compact-content benchmark baseline

The new PHASE_INT/PHASE_FRAC arithmetic lines added to
gsd-core/workflows/execute-phase.md shifted its committed compaction-ratio
baseline. Regenerate via `node scripts/benchmark-compact-content.cjs --write`.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* docs(#4619): note the safe_resume_gate arithmetic growth in the test header

The emitted-attribution gate flags execute-phase.md growing 91253 -> 91846
bytes (593 bytes). The growth is the fix: the safe_resume_gate and TDD RED
block now derive PHASE_INT/PHASE_FRAC before computing PHASE_N, so a
decimal/N-segment phase number (e.g. 01.1, 2.3.1) zero-strips its leading
integer segment via base-10 arithmetic instead of forcing the whole value
through $((10#...)) and hitting a hard shell syntax error on the first dot.

A blank line previously separated the Emitted-Drift-Ack-Growth trailer from
the Co-Authored-By trailer below it, which splits git's trailer-block
detection: only the last contiguous non-blank run of Key: Value lines at the
end of a commit message is recognized as trailers, so the growth ack was
silently read as ordinary body text and the differential-attribution gate
failed with the growth unacknowledged. Joining the two trailers into one
contiguous block fixes it.

Emitted-Drift-Ack-Growth: execute-phase.md — adds PHASE_INT/PHASE_FRAC derivation to the safe_resume_gate and TDD RED commit-scope grep so a decimal/N-segment phase number zero-strips its leading integer segment via base-10 arithmetic instead of failing on a non-numeric value (#4619)
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* test(#4208): replace chmod-based restore-failure injection with a root-proof git shim

`tests/commit-files-deletion.test.cjs`'s two restore-failure tests simulated
an unwritable index via a `post-index-change` hook running `chmod a-w` on
the git dir. That relies on the OS enforcing the *owner's own* permission
bits against itself, which uid 0 (a routine identity inside this repo's
Docker-based gsd-test benches) does not: every DAC check short-circuits true
for root, so the write the chmod meant to block silently succeeds, the
restore comes back clean, and the disclosure/rollback behavior under test
never actually gets exercised.

This is CLAUDE.md's own named anti-pattern for I/O-failure injection
("Cross-platform test IO-failure injection" — chmod tricks fail under root
Docker/CI). It is confirmed as the actual root cause here, not a production
defect: `src/commands.cts`'s `restoreRemovedEntries`/rollback-disclosure
logic (added by #4253, merged just before this run) was hand-traced and
manually reproduced end to end on an unprivileged workstation against a
freshly built `gsd-core/bin/lib/commands.cjs`, and it already produces
exactly the `staging_failed` + "could not be restored" / "could NOT be
restored during rollback" results both tests assert. The other
`post-index-change`-based tests in this file (a `sleep` to force a timeout;
a real `update-index` to flip a restored entry's mode) are unaffected
because neither depends on a permission check — consistent with only the
two chmod-based tests failing on the real remote run.

Replaces the chmod fixture with a fake `git` placed ahead of the real one on
PATH that fails only `update-index --add --cacheinfo` — the one call the
restore makes — unconditionally, regardless of privilege level. Every other
git invocation execs straight through to the real binary, so the rest of
each scenario (`rm --cached`, the restore's own `ls-files` verification,
etc.) is exercised exactly as before.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* chore(#4619): backfill changeset pr number to 4644

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(#4619): feed the bash fixture script via stdin, not argv, to fix Windows CI

Passing the script as a `-c "<script>"` argv element made it subject to
Windows' CreateProcess command-line argument encoding, which silently
dropped the escaped-dot backslashes before bash ever saw them (observed on
PR #4644's windows-latest CI shard: `1\.1` came back as `1.1`). Feeding the
same script via stdin instead removes argv entirely from the transport, so
there is nothing for Windows to re-encode. POSIX behavior is unchanged.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

---------

Co-authored-by: sim <sim@local>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

scripts/lib/macos-conformance-tier.generated.cjs

@@ -61,6 +61,7 @@ module.exports = {
   "tests/effort-sync-installed-runtime.test.cjs",
   "tests/emitted-attribution.test.cjs",
   "tests/ensure-runtime-build.test.cjs",
+  "tests/execute-phase-decimal-arithmetic.test.cjs",
   "tests/executed-plan.test.cjs",
   "tests/executor-mvp-tdd-section.test.cjs",
   "tests/external-job.test.cjs",

scripts/lib/platform-conformance-tier.generated.cjs

@@ -158,6 +158,7 @@ module.exports = {
   "tests/estimate-calibrate.test.cjs",
   "tests/estimate-loop-convergence.test.cjs",
   "tests/execute-mvp-tdd-gate.test.cjs",
+  "tests/execute-phase-decimal-arithmetic.test.cjs",
   "tests/execute-phase-wave.test.cjs",
   "tests/execute-phase-worktree-guard.test.cjs",
   "tests/execute-plan-update-codebase-map-diff-base.test.cjs",

scripts/lint-phase-id-drift.cjs

@@ -234,10 +234,30 @@ function findBranchSlugFallbackDrift(text) {
   return out;
 }
 
-// #4634: ban base-10-forced shell arithmetic (`$((10#...))`) on any variable —
-// this construct is exactly the pattern that breaks on a decimal or
-// multi-segment phase id, so any occurrence is banned outright, full stop.
-const SHELL_PHASE_ARITH_DRIFT_RE = /\$\(\(\s*10#/;
+// #4634: ban base-10-forced shell arithmetic (`$((10#...))`) on a variable
+// that still carries a possibly-decimal/multi-segment phase id — this
+// construct is exactly the pattern that breaks on a value like `08.5`. The
+// capture group grabs the token immediately inside the parens (after an
+// optional `$` and/or `{`, stripping a trailing `}`) so callers can inspect
+// *which* variable is being coerced, not merely that the substring occurred.
+//
+// Refined post-#4619: the original blunt "ban `$((10#` outright" version
+// over-fired on three false-positive classes once #4619's fix landed:
+//   1. Prose mentioning the literal pattern in a full-line `#`-comment
+//      (filtered by the caller, not this regex — see below).
+//   2. `$((10#$PHASE_INT))` / `$((10#$SPOT_PHASE_INT))` — arithmetic on the
+//      NOW-safe variable the #4619 fix produces via `PHASE_INT=${PHASE_NUMBER%%.*}`;
+//      a `%%.*`-stripped value can never contain a dot, so base-10 arithmetic
+//      on it can never hit the #4619 syntax-error class. Any name ending in
+//      `_INT` (case-insensitive) is that established "already reduced to a
+//      safe integer" convention.
+//   3. `$((10#{plan_padded}))` / `$((10#${PLAN_ID}))` — plan ids are plain
+//      integers and were never in scope; this rule only polices variables
+//      that carry a *phase* id.
+// So a match is only a violation when the captured name contains `phase`
+// case-insensitively (it is phase-carrying) AND does not end in `_int`
+// case-insensitively (it has not already been reduced to a safe integer).
+const SHELL_PHASE_ARITH_DRIFT_RE = /\$\(\(\s*10#\$?\{?([A-Za-z0-9_]+)\}?/;
 
 // A markdown comment can't easily carry a `//` line, so the sanction for the
 // shell-arithmetic rule is an HTML comment on the nearest preceding non-blank
@@ -246,15 +266,25 @@ const MD_OWNER_RE = /^\s*<!--.*phase-id-owner:/;
 
 /**
  * Pure: find every unsanctioned `$((10#...))` base-10-forced shell arithmetic
- * site in `text`. Sanctioned by an HTML comment `<!-- phase-id-owner: ... -->`
- * on the nearest preceding non-blank line. Returns [{ line, found }].
+ * site in `text` that still coerces an un-reduced phase-carrying variable.
+ * Skips full-line `#` comments outright (pure prose mentioning the pattern,
+ * not executable code), and skips any captured variable name that either
+ * doesn't contain `phase` (never in scope — e.g. plan ids) or already ends
+ * in `_int` (the #4619-fix convention for "safely stripped to an integer").
+ * Sanctioned by an HTML comment `<!-- phase-id-owner: ... -->` on the
+ * nearest preceding non-blank line. Returns [{ line, found }].
  */
 function findShellPhaseArithDrift(text) {
   const out = [];
   const lines = text.split('\n');
   for (let i = 0; i < lines.length; i++) {
-    const m = SHELL_PHASE_ARITH_DRIFT_RE.exec(lines[i]);
+    const line = lines[i];
+    if (/^\s*#/.test(line)) continue;
+    const m = SHELL_PHASE_ARITH_DRIFT_RE.exec(line);
     if (!m) continue;
+    const name = m[1];
+    if (!/phase/i.test(name)) continue;
+    if (/_int$/i.test(name)) continue;
     if (isSanctionedByPrecedingComment(lines, i, MD_OWNER_RE)) continue;
     out.push({ line: i + 1, found: m[0] });
   }