Update Dependencies

Update Dependencies

Run all 6 checks in order. Auto-fix safe issues, report risky ones.

Vault root: ~/Library/Mobile Documents/iCloud~md~obsidian/Documents

1. Vault-rag index (AUTO-FIX)

import json, os
path = os.path.expanduser('~/Code/vault-rag/index_state.json')
vault = os.path.expanduser('~/Library/Mobile Documents/iCloud~md~obsidian/Documents')
with open(path) as f:
    data = json.load(f)
before = len(data)
stale = [p for p in data if not os.path.exists(os.path.join(vault, p))]
for s in stale:
    del data[s]
if stale:
    with open(path, 'w') as f:
        json.dump(data, f, indent=2)

Run this via python3 -c "...". Report: Removed N stale entries (M remaining).

2. Wikilinks (REPORT)

1. Build a set of all .md file stems (without extension) across the entire vault
2. Grep for \[\[([^\]]+)\]\] in 30_knowledge/, 50_areas/, 20_projects/, 00_inbox/
3. For each wikilink, extract the target (before | if aliased)
4. Check if target exists in the file stems set
5. Skip books.md and papers.md — these have intentional unresolved refs
6. Report broken links grouped by file, with count

3. Config file paths (REPORT)

Scan these files for dead paths:

• ~/.claude/CLAUDE.md
• Vault CLAUDE.md
• MEMORY.md (in the project memory dir)
• All .md files in the project memory dir

For each file:

1. Extract paths — look for backtick-wrapped paths (`~/...`, `vault ...`), and bare paths starting with ~/, /Users/, or vault-relative paths
2. Resolve ~ to home dir, vault-relative paths to vault root
3. Check each path exists on filesystem
4. Skip lines that are clearly historical — lines containing words like "Phase", "removed", "deleted", "renamed", "merged", "archived", "was", "were", "formerly", past-tense context
5. Report dead paths as file:line → dead_path

4. LaunchAgent plists (REPORT)

1. Read all ~/Library/LaunchAgents/*.plist files
2. For each, extract the script path from <key>ProgramArguments</key> array
3. Check if the script file exists on disk
4. Skip paths that are system commands (/bin/bash, /usr/bin/env, etc.)
5. Report dead script paths as plist_name → dead_path

5. Dir tree Quick Lookup (REPORT)

1. Read 50_areas/personal/directory_tree.md
2. Find the Quick Lookup table
3. For each row, extract the path from the Location column
4. Resolve vault-relative paths (e.g., vault 30_knowledge/) to full paths
5. Check if the referenced file/dir exists
6. Report any rows where the path doesn't resolve

6. Frontmatter compliance (REPORT)

1. In 30_knowledge/: count files missing origin, type, or status (skip _index.md)
2. In 00_inbox/: count files with no YAML frontmatter at all (skip _index.md)
3. Report counts only (not individual files — keep it concise)

Output Format

Present results as:

## Dependency Sweep Results

### Auto-fixed
- Vault-rag: removed N stale entries (M remaining)

### Needs Attention
| Check             | Issues | Details                    |
|-------------------|--------|----------------------------|
| Broken wikilinks  | N      | file1.md (2), file2.md (1) |
| Dead paths        | N      | source:line details        |
| LaunchAgent       | N      | plist → dead_path          |
| Dir tree drift    | N      | row details                |
| Frontmatter gaps  | N      | 30_knowledge: X, inbox: Y  |

### Summary
N issues auto-fixed, M issues need attention.

If a check finds 0 issues, show "Clean" in the Details column. Do NOT omit clean rows — show all 5 checks for completeness.

Rules

• NEVER edit LaunchAgent plists, CLAUDE.md, or MEMORY.md — only report
• NEVER delete vault files — only report
• Auto-fix is limited to: vault-rag index_state.json stale entry removal
• Do NOT flag books.md or papers.md wikilinks — those are intentionally unresolved
• Do NOT flag historical/past-tense references in MEMORY.md — those document what happened, not live paths