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/script tallies, and more.

When to Use

• After significant project work (new files, completed milestones, structural changes)
• During $session-recap 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 AGENTS.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 AGENTS.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. Script count — count *.sh scripts in hooks/ (if present)
9. Skill lengths — wc -l skills/*/SKILL.md to identify bloated skills

Leanness data (all projects):
10. AGENTS.md line count — wc -l AGENTS.md
11. AGENTS.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 AGENTS.md content duplicates what's already in README.md, docs/, or .context/ files

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/script counts	(Task Management only) Compare actual count vs documented numbers in AGENTS.md, README.md, and .tex files
Venue/target info	If AGENTS.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
AGENTS.md	> 200 lines total	Current line count	Extract reference sections to docs/, replace with pointers (see lean-agents-md rule)
AGENTS.md sections	Any ## section > 15 lines of reference material	Section name + line count	Extract to docs/ with a one-line summary + link
AGENTS.md duplication	Content duplicated from README/docs/.context	Which content is duplicated and where	Keep only the pointer in AGENTS.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

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]:

AGENTS.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:
  - AGENTS.md: 237 lines (threshold: 200) — ## Assessment section is 42 lines of guidelines
  - README.md: OK (189 lines)
  - skills/paper-writing/SKILL.md: 382 lines (threshold: 300) — conference checklists could move to references/

If nothing is stale, report that and stop.

Step 5: Ask for Confirmation

Ask the user directly to approve, modify, or skip each group:

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

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:
  AGENTS.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-recap — offers to run this skill at Step 3.5
• $update-project-doc — Task Management-specific superset: propagates counts across all TM docs including LaTeX files. Run after this skill when in the TM project.
• $update-focus — updates current-focus.md (different purpose: session state, not doc accuracy)