Update Project Doc — Refresh Stale Documentation

Scan a project's documentation files and update sections that have drifted from reality: file trees, timestamps, bibliography counts, next steps, skill/hook tallies, and more.

When to Use

• After significant project work (new files, completed milestones, structural changes)
• During session-close when offered
• When the user says "update project docs", "refresh docs", "sync my docs", "update my README"
• Periodically to keep documentation accurate

What It Does NOT Do

• Never rewrites research content (hypotheses, arguments, literature, design decisions)
• Never deletes sections — only updates factual/structural content within existing sections
• Never creates new documentation files — only updates existing ones

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Protocol

Step 1: Detect Documentation Files

Find all documentation files in the project:

1. Check for CLAUDE.md in project root
2. Check for README.md in project root
3. Scan docs/ and docs/*/ for .md files containing file trees or counts
4. Note which files exist — only update what's present

Special case: Some projects (e.g., the political information paper) have no CLAUDE.md because they use a committed README.md as their primary project documentation instead. This is intentional for repos meant to be shared or published. In these cases, treat README.md as the main documentation file and apply all the same checks to it.

Read each detected file to understand its current content.

Step 2: Gather Current State

Collect the actual state of the project:

1. File tree — use ls -R or Glob to build the actual directory structure (respect .gitignore patterns, skip out/, __pycache__/, .venv/, node_modules/)
2. Recent git history — git log --oneline -20 for recent commits
3. Session logs — read the latest 1-2 files in log/ (if the directory exists)
4. Bibliography count — count entries in any .bib file(s): grep -c '@' *.bib
5. Symlink targets — readlink on any documented symlinks
6. Context files — read .context/current-focus.md or .context/project-recap.md if present

Task Management only (detected by presence of skills/ directory): 7. Skill count — count directories in skills/ that contain SKILL.md 8. Hook count — count .sh files in hooks/ (if present) 9. Skill lengths — wc -l skills/*/SKILL.md to identify bloated skills

Leanness data (all projects): 10. CLAUDE.md line count — wc -l CLAUDE.md 11. CLAUDE.md section sizes — count lines per ## section 12. README.md line count — wc -l README.md 13. SKILL.md line counts — (Task Management only) wc -l skills/*/SKILL.md 14. Duplication scan — check if CLAUDE.md content duplicates what's already in README.md, docs/, or .context/ files 15. Agent line counts — wc -l .claude/agents/*.md (if present) 16. Context file line counts — wc -l .context/*.md (if present)

Step 3: Run Staleness Checks

Compare gathered state against documented content. Flag any mismatches:

Check	How to Detect
File tree	Generate actual tree, compare against any tree/structure block in docs (look for ``` blocks or indented listings with file paths)
Timestamps	Flag "Last updated", "w/c", or date stamps older than 7 days
Bibliography count	Compare actual .bib entry count vs any documented count (e.g., "42 references")
Next steps / roadmap	Cross-reference items against recent commits and session logs — flag items that appear completed
Manuscript status	Flag sections marked "TODO", "incomplete", or "placeholder" that now have content
Symlinks	Verify documented symlink targets still resolve with readlink
Skill/hook counts	(Task Management only) Compare actual count vs documented numbers in CLAUDE.md, README.md, and .tex files
Venue/target info	If CLAUDE.md documents a target journal, check it matches .context/projects/_index.md (if accessible)

Step 3b: Leanness Audit

Using the data gathered in Step 2 (items 10-14), check infrastructure file sizes against thresholds. This applies to all projects, not just Task Management.

File	Threshold	What to flag	Fix
CLAUDE.md or AGENTS.md	Exceeds the lean-guidance-files budget	Current line and word count	Extract reference sections to docs/, replace with pointers
CLAUDE.md sections	Any ## section > 15 lines of reference material	Section name + line count	Extract to docs/ with a one-line summary + link
CLAUDE.md duplication	Content duplicated from README/docs/.context	Which content is duplicated and where	Keep only the pointer in CLAUDE.md
README.md	> 300 lines total	Current line count	Extract long sections to docs/
SKILL.md files	> 300 lines each (TM only)	File name + line count	Move templates/examples/report formats to references/ or templates/ subdirectory
Project agents (.claude/agents/*.md)	> 400 lines each	File name + line count	Extract verbose prompt sections to companion files
Context files (.context/*.md)	> 200 lines each	File name + line count	Archive stale content, keep current

What counts as "reference material" (extractable): assessment guidelines, detailed literature notes, long examples, report templates, checklists, reviewer feedback.

What does NOT count (keep in place): safety rules, conventions, folder structure trees, session continuity pointers.

Present leanness findings separately from staleness findings in Step 4.

Step 4: Propose Changes

Present findings grouped by file:

Staleness report for [Project Name]:

CLAUDE.md:
  - File structure tree is outdated (missing: X, Y; removed: Z)
  - Skill count says 23, actual is 26
  - "Last updated" date is 3 weeks old

README.md:
  - Directory structure block needs updating
  - Next steps: "Write introduction" appears completed (commit abc1234)
  - Bibliography count says 38, actual is 42

docs/overview.md:
  - No issues detected

Leanness:
  - CLAUDE.md: 237 lines (threshold: 200) — ## Assessment section is 42 lines of guidelines
  - README.md: OK (189 lines)

If nothing is stale, report that and stop.

Step 5: Ask for Confirmation

Step 5a: Staleness Fixes

Use the available structured-question mechanism to let the user approve, modify, or skip staleness fixes:

• Apply all — update everything proposed
• Select by file — choose which files to update
• Skip — make no changes

Step 5b: Offer Leanness Fixes

If Step 3b found leanness issues, present each as an individually actionable item:

Leanness fixes available:

| # | File | Issue | Current | Fix |
|---|------|-------|---------|-----|
| 1 | CLAUDE.md | >200 lines | 237 | Extract ## Assessment section → docs/ |
| 2 | skills/X/SKILL.md | >300 lines | 382 | Move checklists → references/ |

Use the available structured-question mechanism with multiSelect: true:

• Question: "Which leanness fixes do you want to apply?"
• One option per fix with current size and proposed outcome
• Include an "All of them" option as the first choice

Do not defer or merely report leanness findings. Always present them as actionable items alongside staleness fixes.

Step 6: Apply and Report

For each approved change:

1. Use targeted Edit operations — never rewrite entire files
2. Preserve all surrounding content
3. When updating file trees, match the existing formatting style (├──, |--, indented, etc.)
4. When updating counts, find the exact number and replace it
5. When marking next-step items as done, use strikethrough (item) rather than deleting

After all edits, print a summary:

Updated project docs:
  CLAUDE.md:  file tree, skill count (23 → 26)
  README.md:  directory structure, bib count (38 → 42), 1 next-step marked complete
  Total: 5 edits across 2 files

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Key Rules

1. Targeted edits only — never rewrite entire files. Use Edit with precise old_string / new_string.
2. Preserve research content — hypotheses, questions, literature reviews, design decisions, and arguments are sacred. Only update factual/structural sections.
3. Always show before applying — never make silent edits. The proposal step is mandatory.
4. Match existing style — if the project uses ├── trees, don't switch to |--. If counts use "X total", don't change to "X skills".
5. Works in any project — not just Task Management. Adapt checks to what's present.
6. Idempotent — running twice in a row should produce no changes the second time.

Cross-References

• session-close — offers to run this skill at Step 3.5
• sync-repo private — Task Management-specific superset: propagates counts across all private TM docs including LaTeX files. Run after this skill when in the TM project.
• vault sync (edit vault files directly) — syncs state to the central context library (complementary; run after this)
• update-focus — updates current-focus.md (different purpose: session state, not doc accuracy)