indexion-wiki

name	indexion-wiki
description	Project wiki lifecycle — create pages, track source changes with ingest, update stale pages, lint structural integrity, detect code-to-doc drift with reconcile, and manage search indexes. A runbook for navigating and maintaining the wiki as an agent.

indexion wiki

indexion's wiki system maintains a knowledge base at .indexion/wiki/ as a collection of Markdown files governed by a wiki.json manifest.

A wiki page is not just a .md file

A wiki page consists of four synchronized artifacts:

Artifact	File	Updated by
Page content	<id>.md	wiki pages add, wiki pages update
Manifest entry	wiki.json	wiki pages add, wiki pages update
Search index	vectors.db, search-sections.json, tfidf-vocabulary.json	wiki pages update, wiki index build --full
Audit log	log.json	Every wiki-modifying command

wiki pages update updates all four at once. Editing the .md file directly updates only the first. The other three become stale — search returns old results, the manifest carries wrong provenance, and the log has no record of the change.

If you edit a .md directly (e.g. via Edit tool), you must immediately follow up:

indexion wiki pages update \
  --id=<page-id> \
  --content=.indexion/wiki/<page-id>.md \
  --sources="<comma-separated sources from wiki.json>" \
  --provenance=synthesized \
  --actor="agent:claude" \
  --wiki-dir=.indexion/wiki

Every wiki page also carries two provenance fields in the manifest:

• provenance: "extracted" | "synthesized" | "manual"
• last_actor: "indexion" | "agent:<name>" | "user"

Command Structure

indexion wiki
  ├── pages
  │   ├── plan    -- propose page structure (init-like)
  │   ├── add     -- create a new page (writes .md + manifest + index + log)
  │   ├── update  -- update an existing page (writes .md + manifest + index + log)
  │   └── ingest  -- detect stale pages by hashing sources
  ├── index
  │   └── build   -- rebuild index.md (and optionally vectors.db)
  ├── lint        -- structural integrity checks (no LLM needed)
  ├── export      -- export to GitHub/GitLab wiki format
  ├── import      -- import from GitHub/GitLab wiki format
  └── log         -- operation audit trail

Navigating the Wiki (as an agent)

Before reading individual pages, start with the index:

# Generate or regenerate index.md — the entry point for navigation
indexion wiki index build --wiki-dir=.indexion/wiki

# Then read it
cat .indexion/wiki/index.md

index.md lists pages by category and identifies hub pages (most-linked pages). Hub pages are the best starting points for understanding an unfamiliar codebase.

Writing a New Page

# 1. Write content to a temp file
cat > /tmp/my-page.md << 'EOF'
# My Page Title
...content...
EOF

# 2. Register it — this writes .md, updates wiki.json, updates search index, appends log
indexion wiki pages add \
  --id=my-page \
  --title="My Page Title" \
  --content=/tmp/my-page.md \
  --sources="src/my-module/" \
  --provenance=synthesized \
  --actor="agent:claude" \
  --wiki-dir=.indexion/wiki

The --sources field links the page to source files for change tracking. Always specify it — pages without sources are invisible to wiki pages ingest.

Updating an Existing Page

# 1. Write new content to a temp file
cat > /tmp/updated.md << 'EOF'
# Updated Page
...new content...
EOF

# 2. Update — this overwrites .md, updates wiki.json metadata,
#    incrementally updates the search index, and appends to log.json
indexion wiki pages update \
  --id=existing-page \
  --content=/tmp/updated.md \
  --sources="src/my-module/,src/other/" \
  --provenance=synthesized \
  --actor="agent:claude" \
  --wiki-dir=.indexion/wiki

Expected output: Updated page 'existing-page' (search index updated)

Detecting What Needs Updating

# Find pages whose source files have changed since the last run
indexion wiki pages ingest --wiki-dir=.indexion/wiki

# Preview without recording the new hash state
indexion wiki pages ingest --dry-run --wiki-dir=.indexion/wiki

ingest hashes every source file listed in wiki.json and compares against .indexion/wiki/ingest-manifest.json. It outputs an update task list but does not rewrite pages — that is the agent's responsibility.

Workflow:

1. Run wiki pages ingest to get the task list.
2. For each task, read the changed source files.
3. Update the wiki page with wiki pages update.
4. Re-run ingest — it should report 0 pages needing attention.

Verifying Structural Integrity

# Run all 6 structural checks
indexion wiki lint --wiki-dir=.indexion/wiki

Check	What it finds
Broken links	wiki://page-id references to pages that don't exist
Orphan pages	Pages unreachable from nav tree and not linked by any other page
Missing cross-references	Pages sharing source files that don't link to each other
Stale sources	sources paths that no longer exist on disk
Empty pages	Pages with near-zero content
Manifest-file mismatch	wiki.json entries with no .md file (or vice versa)

After writing new pages, always run wiki lint and fix any issues before finishing.

Cross-reference warnings are common when related concepts are split across pages. Fix them by adding a ## See Also section with wiki://page-id links.

Verifying Content Accuracy (plan reconcile)

wiki lint catches structural problems. plan reconcile catches semantic drift — whether the code symbols described in a wiki page still exist and whether the code has changed since the page was last written.

Always target the project root (.). The --doc flag restricts which documents participate, but the target directory determines the code symbol universe. Targeting a subdirectory shrinks the symbol set and produces zero-fragment reports.

indexion plan reconcile \
  --doc='.indexion/wiki/*.md' \
  --doc-spec=markdown \
  --format=md \
  .

Reading the report

Summary — key metric is New logical reviews (fresh drift since last run).

Suggested Review Groups — the actionable core:

Category	Meaning	Action
stale_doc	Code changed after the wiki page was last updated	Update the page via wiki pages update
missing_doc	Code symbols with no matching wiki coverage	Add coverage or create a new page via wiki pages add
review_both	Wiki is newer than code	Verify the wiki content is correct; this is the expected state after a maintenance cycle

Each group lists affected symbols and the Docs: wiki pages involved. Groups without a Docs: line mean no wiki page covers that module.

Residual candidates that persist after maintenance

Reconcile candidates never reach zero. Three sources of persistent candidates:

1. Modules without wiki pages produce missing_doc. Create pages if coverage is needed.
2. Qualified method names (Type::method in wiki) don't match bare symbol names (method in code). Verify by grepping the wiki for the symbol name before adding entries.
3. Same-name symbols across modules (get, tokenize, to_json_string) cause cross-module false positives. Check which module the wiki page actually describes.

Track New logical reviews as the convergence metric. When it reaches zero, all actionable drift has been addressed.

Full Wiki Maintenance Cycle

# 1. Detect stale pages (source files changed)
indexion wiki pages ingest --wiki-dir=.indexion/wiki

# 2. Read the index to understand the wiki structure
cat .indexion/wiki/index.md

# 3. For each stale page: read changed sources, write new content to temp file,
#    then update through the command (NOT by editing .md directly)
indexion wiki pages update --id=<page-id> --content=/tmp/updated.md \
  --sources="..." --provenance=synthesized --actor="agent:<name>" \
  --wiki-dir=.indexion/wiki

# 4. Verify structural integrity
indexion wiki lint --wiki-dir=.indexion/wiki

# 5. Verify content accuracy — target project root, iterate until NLR=0
indexion plan reconcile \
  --doc='.indexion/wiki/*.md' \
  --doc-spec=markdown \
  --format=md \
  .
# → Fix stale_doc groups first. Re-run. Expect 2-3 rounds.
# → For each fix, use `wiki pages update`, not direct .md edits.

# 6. Regenerate the navigation index
indexion wiki index build --wiki-dir=.indexion/wiki

# 7. Confirm everything is current
indexion wiki pages ingest --dry-run --wiki-dir=.indexion/wiki

Planning a New Wiki from Scratch

When the wiki doesn't exist yet or needs a structural overhaul:

# Analyze the project and generate a page structure proposal
indexion wiki pages plan --format=md <project-dir>

# Then execute the plan: add each proposed page
indexion wiki pages add --id=<id> --title="..." --content=/tmp/page.md \
  --sources="..." --provenance=synthesized --actor="agent:<name>"

No initialization step is needed. The first wiki pages add call automatically creates .indexion/wiki/ and an empty wiki.json manifest. There is no separate wiki init command.

wiki pages plan uses the CodeGraph to propose concept-based pages, not file-based ones. Prefer concept pages (e.g., "KGF System") over file pages (e.g., "src/kgf/lexer/lexer.mbt").

Building the Search Index

# Build navigation index only (index.md)
indexion wiki index build --wiki-dir=.indexion/wiki

# Build navigation + vector search index (vectors.db)
indexion wiki index build --full --wiki-dir=.indexion/wiki

# Preview index.md without writing
indexion wiki index build --dry-run --wiki-dir=.indexion/wiki

With --full, indexion search .indexion/wiki/ will use the pre-built vectors instead of rebuilding from scratch on each query.

Checking the Audit Trail

# Recent operations
indexion wiki log --wiki-dir=.indexion/wiki --tail=20

# Full log as JSON
indexion wiki log --wiki-dir=.indexion/wiki --json

Every pages add, pages update, lint, pages ingest, and index build call appends to .indexion/wiki/log.json. Use the log to verify that previous agent runs completed correctly, or to understand why a page was last modified.

Key Pitfalls

Backtick-quoted wiki:// references are not links. The lint checker correctly ignores wiki:// in code spans. Use bare wiki://page-id or Markdown links [Title](wiki://page-id) to create real cross-references.

wiki pages ingest manifests state at the time of the last run. If you add new source files to a page's sources list via pages update, the next ingest run will show that page as needing attention (because the new sources have no recorded hash). This is expected behavior — run ingest again after the update to record the baseline.