[savvides]

Fixes

• idstack-ste-check: a folder scan skips .markdown files #173 idstack-ste-check folder scan now includes .markdown. Test in test/test-ste-check.py, docs updated.
• idstack-status: the dashboard and the readiness table read different data #172 part 2 (part 1, the 200-line window, was already fixed on main). A skill with a completed timeline event but a missing, 0 or non-int manifest score is NEEDS-WORK, and the verdict says "quality review has no score in the manifest" (same for accessibility). Same fail-closed pattern as red_known. 2 new tests in test/test-status.sh.
• idstack-learnings log replaces a caller's ts; idstack-timeline-log keeps it #171 Decision: keep the caller's ts. idstack-learnings log uses setdefault, the same as idstack-timeline-log. Header, docs and an integration test updated.
• Atomic writes leave the manifest and reports at mode 0600 #190 idstack-manifest-merge and idstack-report-section already kept the file mode on main (copymode / umask). The remaining bug was the seed from idstack-migrate --init (mode 0600). It now has 0666 & ~umask. Tests: under umask 022 a new manifest and a merge leave 0644, and an existing 0640 file stays 0640.
• Skills run in $HOME write .idstack/ next to the global profile #178 Script-level guard instead of preamble text: idstack-manifest-merge and idstack-migrate --init write nothing and exit 9 when the course folder (the folder that holds .idstack/) is $HOME (symlinks resolved). Every skill gets it, with no model step to skip.
• Two sessions in one course folder can lose manifest updates #179 Reproduced first (see below). Then: fcntl.flock exclusive lock on .idstack/.manifest.lock from read to write; new --expect-updated <ts> (exit 8, nothing written); the report draft is now .idstack/.report-section.<skill>.md in templates/preamble.md (the only template change; skills regenerated; the zsh test passes <skill>=needs-analysis).

Exit-code deviation from the task text

Exit 7 of idstack-manifest-merge already means "manifest from a newer idstack", so I could not use 7 for the HOME guard. HOME guard is 9 (merge and migrate), --expect-updated is 8, as specified. Both are in the script header and docs/cli-reference.md.

#179 reproduction

Two background loops, 50 merges each, different sections (quality_review, red_team_audit), 5 rounds, final value should be 50 and 50.

• Before the lock: lost updates in 4 of 5 rounds (for example quality=48, 49, 45, red=49).
• After the lock: 0 of 5 rounds lose an update.
• Stale read (read updated, another merge writes, first merge writes back): reproduced by test; with --expect-updated it exits 8 and the manifest is unchanged.

Tests

• Mutation cases 66a-66i, run from a frozen copy: 9 guarded, 0 not guarded. The stale-anchor check over the whole file: 0 ERROR (200 cases matched).
• Suites: smoke 655/655, integration 59/59, test-setup 10/10, test-status 34/34, test-manifest-merge 53/53, test-skill-shell-zsh 161/161, test-doctor 18/18, test-ste-check 37 OK, test-report-section 41 OK, test-extension all pass, check-doc-accuracy exit 0.
• CLAUDE.md counts: integration 59, status 34.

Not verified / known limits

• #171: I could not remove the decision-needed label (gh issue edit was blocked in this session). Please run gh issue edit 171 --remove-label decision-needed.
• Two sessions that run the same skill in one folder still share a draft (the name has the skill, not the session).
• --expect-updated has a 1-second resolution (updated is in seconds). No skill template passes it yet: this PR adds the option only, and I did not edit the templates beyond the scratch name.
• The lock uses fcntl (macOS and Linux only). The canvas-push/ scratch name in Two sessions in one course folder can lose manifest updates #179 is not changed (not in the task).
• The mutation case 66g depends on a race, so it relies on 40 writes for each of 2 writers. It was GUARDED in my run.
• Not run: the full 2.5 h mutation suite, Windows, the Claude desktop app.

Closes #173
Closes #172
Closes #171
Closes #190
Closes #178
Refs #179

#179: the lock and --expect-updated are here. The skill templates pass --expect-updated in #197. The canvas-push/ scratch folder, and two sessions that run the same skill in one folder, still share a name. I close #179 by hand after both PRs merge, with these limits on the issue.

#178: the guard is on the manifest write path only. idstack-timeline-log, idstack-learnings log and idstack-report-section init can still create files under ~/.idstack.

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