Post-Actions

Shared by all modes. Execute after any mode completes successfully. Step 3 derives exactly which files this run touched by diffing the current working tree against the pre-mode baseline captured in Mode Routing.

1. README Update -- if ./research/README.md was already dirty in the pre-mode baseline, report to the user: ./research/README.md -- pre-existing uncommitted changes present; this run's README update will not be committed before proceeding -- the update below still needs to happen so the mode's own entry is recorded, but step 3 will exclude README.md from this run's commit. Otherwise, add or update entries in ./research/README.md category tables as usual. This restates the README step each mode's own flow already gates (Default step 6d, Batch UpdateAll/Partial, Rerun UpdateDate(s)) -- do not run it as a fresh, ungated pass. Do not add a row, or refresh the Last Updated date on an existing row, for any entry marked "created with issues" or "refreshed with issues" earlier in this run; that entry's README state stays exactly as it was before this run started. Entry Review sets that mark after this run already wrote the row, so for an entry it marks, restore that entry's row to the version in git show HEAD:./research/README.md -- deleting the row outright when that version has none. That command is the pre-run state only when README.md was clean in the baseline; when it was already dirty, this run's README changes are excluded from the commit by this step anyway, so report the mark and leave the file alone

2. Backlink Repair -- deterministically repair the bidirectional cross-reference graph across the whole vault, not just entries this run touched:

   Pass --exclude {path} once per path that was already dirty in the pre-mode baseline (see Mode Routing). The repair writes its reciprocal row into the cited entry, so without this it can write into another contributor's uncommitted work. An excluded file is still scanned and its asymmetric pairs are still reported -- only the write is withheld, counted in stdout JSON as backlinks_excluded. Step 3 below still filters those paths out of the commit; --exclude is what keeps them unmodified on disk in the first place.

   uv run scripts/run_bounded.py --timeout-seconds 180 -- \
     uv run .claude/skills/research-curator/scripts/validate_research.py check-backlinks ./research --fix \
       --exclude {baseline-dirty-path} ...
   

   Check the result in this order:

   1. Exit code 124 (run_bounded.py's timeout signal): halt Post-Actions and report a timeout unconditionally. A terminated run's partial state is not trustworthy to commit.
   2. Stdout is not one compact JSON object containing integer asymmetric_cross_references: the command crashed before completing its scan rather than reporting a structural result. Halt Post-Actions and report the failure to the user.
   3. Stderr contains a warning: io-error, could not repair ... line: a genuine I/O failure reading or writing a target. Halt Post-Actions and report the exact warning text.
   4. Otherwise: continue to step 3 regardless of this exit code. This covers a warning: structural, could not repair ... line (a malformed entry the script cannot parse, e.g. a Cross-References row with no markdown link). A non-zero scan_skipped_files field belongs here too: those files were dropped from the graph before they could be compared, so asymmetric_cross_references undercounts by whatever they hold, and a positive skip count is on its own enough to make this command exit non-zero. Read each object in skips and report its path, reason, and detail verbatim -- the files are repairable and nothing else in the repo will name them -- then continue. Pass --allow-partial-scan only when a run must exit 0 despite that hole in its coverage; this step never needs it, because it already continues past a non-zero exit. Do not use the edges array to guess which files were modified -- it lists every asymmetric edge found before repair was attempted, not which repairs succeeded. Step 3's diff determines what this command actually changed.

3. Compute the filtered file list -- diff the current working tree against the pre-mode baseline (see Mode Routing) to get every file under ./research/ this run touched:

   git diff --name-only -- ./research/
   git ls-files --others --exclude-standard -- ./research/
   

   Exclude any path that was already dirty in the baseline -- that is another contributor's pre-existing uncommitted work, not something this run produced -- and report it to the user as {path} -- pre-existing uncommitted changes, not touched this run. Call what remains the filtered list; steps 4-6 below use it and nothing else, so a pre-existing dirty file is never linted, staged, or committed by this run.

   The baseline only detects files that were already dirty when it was captured; a concurrent edit starting afterwards is indistinguishable from this run's own write. When another contributor may be editing ./research/ at the same time, run this skill from an isolated worktree -- see rules/commit-cadence-and-worktrees.md.

   If the filtered list is empty (nothing was created, refreshed, or repaired this run -- e.g. a clean Validate Mode pass where the backlink repair also found nothing writable to fix), skip steps 4-6 entirely: there is nothing to lint, commit, or push, and this is not a failure.

4. Lint -- run formatting checks on exactly the filtered list:

   uv run prek run --files [the filtered list]
   

5. Commit -- stage and commit exactly the filtered list, immune to whatever else might already be staged in the working tree. Pass the paths to git commit itself -- a pathless git commit -m commits the entire index, not just these paths:

   git add [the filtered list]
   git commit [the filtered list] -m "docs(research): [action] [resource names]"
   

6. Push -- push to current branch:

   git push -u origin HEAD
   

Commit message actions by mode:

• Default -- add {resource-name} research entry
• Batch -- add {N} research entries
• Rerun -- refresh {resource-name|N entries}
• Validate -- fix validation issues in {resource-name|N entries}