Wiki Status — Audit & Delta

You are computing the current state of the wiki: what's been ingested, what's new since last ingest, and what the delta looks like. This helps the user decide whether to append (ingest the delta) or rebuild (archive and reprocess everything).

Before You Start

Read .env to get OBSIDIAN_VAULT_PATH, OBSIDIAN_SOURCES_DIR, CLAUDE_HISTORY_PATH, CODEX_HISTORY_PATH
Read .manifest.json at the vault root — this is the ingest tracking ledger

The Manifest

The manifest lives at $OBSIDIAN_VAULT_PATH/.manifest.json. It tracks every source file that has been ingested. If it doesn't exist, this is a fresh vault with nothing ingested.

{
  "version": 1,
  "last_updated": "2026-04-06T10:30:00Z",
  "sources": {
    "/absolute/path/to/file.md": {
      "ingested_at": "2026-04-06T10:30:00Z",
      "size_bytes": 4523,
      "modified_at": "2026-04-05T08:00:00Z",
      "source_type": "document",
      "project": null,
      "pages_created": ["concepts/transformers.md"],
      "pages_updated": ["entities/vaswani.md"]
    },
    "~/.claude/projects/-Users-name-my-app/abc123.jsonl": {
      "ingested_at": "2026-04-06T11:00:00Z",
      "size_bytes": 128000,
      "modified_at": "2026-04-06T09:00:00Z",
      "source_type": "claude_conversation",
      "project": "my-app",
      "pages_created": ["entities/my-app.md"],
      "pages_updated": ["skills/react-debugging.md"]
    }
  },
  "projects": {
    "my-app": {
      "source_path": "~/.claude/projects/-Users-name-my-app",
      "vault_path": "projects/my-app",
      "last_ingested": "2026-04-06T11:00:00Z",
      "conversations_ingested": 5,
      "conversations_total": 8,
      "memory_files_ingested": 3
    }
  },
  "stats": {
    "total_sources_ingested": 42,
    "total_pages": 87,
    "total_projects": 6,
    "last_full_rebuild": null
  }
}

Step 1: Scan Current Sources

Build an inventory of everything available to ingest right now:

Documents (from `OBSIDIAN_SOURCES_DIR`)

Glob each directory in OBSIDIAN_SOURCES_DIR for all text files
Record: path, size, modification time

Claude History (from `CLAUDE_HISTORY_PATH`)

Glob: ~/.claude/projects/*/          → project directories
Glob: ~/.claude/projects/*/*.jsonl   → conversation files
Glob: ~/.claude/projects/*/memory/*.md → memory files
Record: path, size, modification time, parent project

Codex History (from `CODEX_HISTORY_PATH`)

Glob: ~/.codex/session_index.jsonl            → session inventory index
Glob: ~/.codex/sessions/**/rollout-*.jsonl    → session rollout transcripts
Glob: ~/.codex/history.jsonl                  → optional local history log
Glob: ~/.codex/archived_sessions/**/rollout-*.jsonl → archived rollouts (if user wants archive coverage)
Record: path, size, modification time, inferred project from cwd when available

Any other sources the user has pointed at previously

Check the manifest for source paths outside the standard directories.

Step 2: Compute the Delta

Compare current sources against the manifest. Classify each source file:

Status	Meaning	Action needed
New	File exists on disk, not in manifest	Needs ingesting
Modified	File in manifest, hash differs from `content_hash`	Needs re-ingesting
Touched	File in manifest, mtime newer but hash unchanged	Skip — content identical, no re-ingest needed
Unchanged	File in manifest, mtime and hash both match	Nothing to do
Deleted	In manifest, but file no longer exists on disk	Note it — wiki pages may be stale

When a manifest entry has no content_hash (older entry), fall back to mtime comparison only.

For Claude history specifically, also compute:

New projects (directories in ~/.claude/projects/ not in manifest)
New conversations within existing projects
Updated memory files

For Codex history specifically, also compute:

New rollout files under sessions/**
Updated session_index.jsonl entries (session title/freshness changes)
Archived rollout delta only when archive coverage is requested

Step 3: Report the Status

Present a clear summary:

# Wiki Status

## Overview
- **Total wiki pages:** 87 across 6 categories
- **Total sources ingested:** 42
- **Projects tracked:** 6
- **Last ingest:** 2026-04-06T11:00:00Z

## Delta (what's changed since last ingest)

### New sources (never ingested): 12
| Source | Type | Size |
|---|---|---|
| ~/Documents/research/new-paper.pdf | document | 2.1 MB |
| ~/.claude/projects/-Users-.../session-xyz.jsonl | claude_conversation | 340 KB |
| ~/.codex/sessions/2026/04/12/rollout-...jsonl | codex_rollout | 220 KB |
| ... | | |

### Modified sources (need re-ingesting): 3
| Source | Last ingested | Last modified | Delta |
|---|---|---|---|
| ~/notes/architecture.md | 2026-04-01 | 2026-04-05 | 4 days newer |
| ... | | | |

### New projects (not yet in wiki): 2
- **tractorex** (3 conversations, 2 memory files)
- **papertech** (1 conversation, 0 memory files)

### Deleted sources (ingested but gone): 0

## Summary
- **Ready to ingest:** 12 new + 3 modified = 15 sources
- **Up to date:** 27 sources unchanged
- **Recommendation:** Append (delta is small relative to total)

Step 4: Recommend Action

Based on the delta, recommend one of:

Situation	Recommendation
Delta is small (<20% of total)	Append — just ingest the new/modified sources
Delta is large (>50% of total)	Rebuild — archive and reprocess everything
Many deleted sources	Lint first — check for stale pages, then decide
First time / empty vault	Full ingest — process everything
User just wants to see status	No action — just report

Tell the user:

"You have X new sources and Y modified sources. I'd recommend [append/rebuild]."
"Want me to [ingest the delta / rebuild from scratch / just look at a specific project]?"

Insights Mode

Triggered when the user asks something like "wiki insights", "what's central in my wiki", "show me the hubs", "cross-domain bridges", "what pages are most important", or "wiki structure". This mode is additive — it doesn't replace the delta report, it analyzes the shape of the wiki itself.

Where the delta report tells the user what's pending, insights mode tells them what they've already built and where the interesting structure lives. Complements wiki-lint (which finds problems) by surfacing interesting structure.

What to compute

First, build the wikilink graph. Glob all .md pages, extract every [[wikilink]], and build:

incoming[page] = count of other pages that link to this page
outgoing[page] = count of pages this page links out to
tags[page] = set of tags from frontmatter
category[page] = directory prefix (concepts/, entities/, skills/, etc.)

You'll reuse this graph across all sections below.

Anchor pages (top hubs). Pages with the most incoming links — the load-bearing concepts.
- Rank all pages by incoming count, take top 10
- For each, note both incoming and outgoing counts: pages with high incoming and high outgoing are connector hubs (most valuable)
- Pages with high incoming but zero outgoing are sink hubs — flag as cross-linker candidates
Bridge pages. Pages that connect otherwise-disconnected tag clusters — removing them would partition the graph. These are often more structurally important than raw hub count suggests.
- For each page P, find pairs of pages (A, B) where:
  - A links to P, B is linked from P (or vice versa)
  - A and B share no tags with each other
  - P is the only path between A's tag cluster and B's tag cluster within 2 hops
- Rank by how many cross-cluster pairs P bridges; show top 5
- Label each: "P bridges [tag-cluster-A] ↔ [tag-cluster-B]"
Tag cluster cohesion. For each tag with ≥ 5 pages, score how tightly the pages within it are interconnected:
- n = number of pages sharing this tag
- actual_links = number of wikilinks between any two pages in this tag group
- cohesion = actual_links / (n × (n−1) / 2) — ratio of actual links to maximum possible
- Fragmented clusters (cohesion < 0.15, n ≥ 5): these pages share a topic but aren't woven together. Surface them as cross-linker targets.
- Show top 5 tags by cohesion (strongest clusters) and bottom 5 (most fragmented)
Surprising connections. Cross-category wikilinks that are non-obvious — scored by how unexpected they are:
- Score each wikilink that crosses category boundaries (e.g., concepts/ → entities/, skills/ → synthesis/):
  - +3 if the linking page or claim is marked ^[ambiguous] (uncertain connection, worth reviewing)
  - +2 if the linking page is marked ^[inferred] (synthesized, not directly stated)
  - +2 if the categories are in different knowledge layers (e.g., concepts ↔ entities more surprising than concepts ↔ concepts)
  - +2 if source page has ≤ 2 total links (peripheral) but target has ≥ 8 (hub) — unexpected reach from edge to center
- Show top 5 scored connections with a plain-language reason for each
Orphan-adjacent suggestions. Pages linked from a top-10 hub but with zero outgoing links of their own. Dead-ends in high-traffic areas — prime cross-linker candidates.
Rough clusters. Group anchor pages by dominant tag. (Simple tag intersection — just for orientation.)
Graph delta since last run. Compare the current link graph to the snapshot stored in the previous _insights.md:
- Read the  line at the bottom of the previous _insights.md (if it exists) — it contains a compact JSON edge list
- Compute: new pages added, pages removed, new wikilinks created, wikilinks removed
- Flag: pages that were isolated last run but now have incoming links ("newly connected: X, Y")
- Flag: pages that lost incoming links since last run ("link target may have been renamed: A, B")
- If no previous snapshot exists, skip this section
Suggested questions. Questions this wiki structure is uniquely positioned to answer — or that reveal gaps:
- From ^[ambiguous] claims: "Resolve: What is the exact relationship between X and Y?"
- From bridge pages: "Explore: Why does P connect [cluster-A] to [cluster-B]?"
- From pages with zero incoming links: "Link: X has no incoming links — what should reference it?"
- From fragmented clusters (cohesion < 0.15): "Audit: Should tag [T] be split into more focused sub-tags?"
- Show up to 7, prioritizing AMBIGUOUS first, then bridge nodes, then isolates

Output

Write the result to _insights.md at the vault root. Overwrite freely — it's regenerable. At the very end, embed a compact graph snapshot as an HTML comment so the next run can diff against it.

# Wiki Insights — <TIMESTAMP>

## Anchor Pages (top 10 hubs)
| Page | Incoming | Outgoing | Note |
|---|---|---|---|
| [[concepts/transformer-architecture]] | 23 | 8 | connector hub |
| [[entities/andrej-karpathy]] | 17 | 0 | sink hub — cross-linker candidate |

## Bridge Pages (top 5)
| Page | Bridges | Cross-cluster pairs |
|---|---|---|
| [[concepts/exponential-growth]] | #ml ↔ #economics | 4 pairs |

## Tag Cluster Cohesion
### Most cohesive (well-linked)
- **#ml** — 12 pages, cohesion 0.41
### Most fragmented (cross-linker targets)
- **#systems** — 7 pages, cohesion 0.06 ⚠️ run cross-linker on this tag

## Surprising Connections (top 5)
- [[concepts/scaling-laws]] → [[entities/gordon-moore]] — score 5
  - Reason: cross-layer (concepts ↔ entities), marked ^[inferred]
- ...

## Orphan-Adjacent (dead-ends near hubs)
- [[concepts/foo]] — linked from 3 hubs, 0 outbound links

## Rough Clusters
- **#ml** — transformer-architecture, attention-mechanism, scaling-laws
- **#systems** — distributed-consensus, raft, paxos

## Graph Delta Since Last Run
- +3 new pages, +11 new wikilinks
- Newly connected: [[concepts/bar]], [[entities/baz]]
- Lost incoming links: [[references/old-paper]] (target may have been renamed)

## Questions Worth Asking
1. Resolve: What is the exact relationship between `scaling-laws` and `moore's-law`? (^[ambiguous] claim)
2. Explore: Why does `exponential-growth` bridge #ml and #economics?
3. Link: `references/foo.md` has no incoming links — what should reference it?
4. Audit: Should tag `#systems` be split? (cohesion 0.06, 7 pages)

<!-- GRAPH_SNAPSHOT: {"nodes":["concepts/foo","entities/bar"],"edges":[["concepts/foo","entities/bar"]]} -->

After writing the file, append to log.md:

- [TIMESTAMP] STATUS_INSIGHTS anchors=10 bridges=N cohesion_checked=T surprising=5 questions=7 delta="+N pages +M links"

When to skip

Vaults with fewer than 20 pages — not enough graph structure. Tell the user and skip.
After a fresh wiki-rebuild — wait until at least one ingest has happened.

Notes

If the manifest doesn't exist, report everything as "new" and recommend a full ingest
This skill only reads and reports — it doesn't modify anything (except writing _insights.md in insights mode, which is regenerable)
The actual ingest work is done by the ingest skills (wiki-ingest, claude-history-ingest, codex-history-ingest, data-ingest)
Those skills are responsible for updating the manifest after they finish

wiki-status