Adopt graphify as the synthesis engine

[Lanzelot1]

Summary

• Delete the hand-rolled wiki pattern (type: wiki pages in knowledge/) and delegate synthesis to graphify, a separate MIT-licensed tool that builds a knowledge graph + wiki from a folder of mixed content.
• knowledge/ keeps its role as the authored layer (source files with type: source). graphify-out/ is the new generated synthesis layer (wiki + graph + report), committed to git except cache/.
• /synthesize becomes a thin wrapper around graphify . --update --wiki; /recall, /status, /sleep, /process-inbox updated accordingly.
• Lock-in mitigations baked in: pinned version, committed portable outputs (markdown + NetworkX JSON), documented swap path (Microsoft GraphRAG or LightRAG).

Why

The /synthesize command was a smaller, manual version of what graphify does end-to-end (extraction → graph → per-community wiki → queryable JSON → MCP server → always-on PreToolUse hook). Keeping both duplicates effort and leaves the manual one weaker. Graphify also adds multi-modal ingest (code AST, PDFs, images, video transcription) and 71.5x token reduction on queries.

Install (one-time, per machine)

These are system-level actions and are not part of this PR. Run them after merging:

pipx install -r requirements.txt           # pins graphifyy==0.4.23
graphify install                            # registers /graphify slash command
graphify claude install                     # enables always-on PreToolUse hook
graphify hook install                       # rebuilds graph on commit
pipx inject graphifyy 'graphifyy[mcp]'      # MCP server deps

Files changed

• .claude/commands/synthesize.md — rewrite as graphify wrapper
• .claude/commands/process-inbox.md — drop wiki-update step
• .claude/commands/recall.md — read graphify-out/GRAPH_REPORT.md first, then query graph
• .claude/commands/status.md — Wiki Health → Graph Layer metrics
• .claude/commands/sleep.md — drop wiki synthesis/staleness, rebuild graph at end; contradiction check against AMBIGUOUS edges
• scripts/validate-frontmatter.sh — drop type: wiki → ## Sources check
• CLAUDE.md — document new flow + swap path
• README.md — rewrite Folders, Slash Commands, and Synthesis Layer sections
• memory/_index.md — remove Wiki Pages section, link graphify-out/GRAPH_REPORT.md and wiki
• .gitignore — ignore graphify-out/cache/ only
• .mcp.json (new) — expose graphify as MCP server
• requirements.txt (new) — pin graphifyy[mcp]==0.4.23

Test plan

• After merge, run the install commands above.
• graphify --version prints 0.4.23.
• /graphify appears as a slash command in Claude Code.
• On a populated knowledge/, /synthesize produces graphify-out/wiki/, graph.json, GRAPH_REPORT.md.
• /status reports graph metrics (nodes, edges, communities, god nodes, AMBIGUOUS count) when graphify-out/ exists.
• /recall "some topic" reads GRAPH_REPORT.md and queries the graph.
• /mcp in a fresh session lists graphify; query_graph returns structured results.
• Post-commit hook rebuilds graphify-out/ after a knowledge/ change.
• scripts/validate-frontmatter.sh passes.
• CI passes (no .mcp.schema.json exists, so .mcp.json is not schema-validated — confirmed intentional).

Swap path (lock-in mitigation)

If graphify stagnates, migration targets are Microsoft GraphRAG or LightRAG. Outputs are plain markdown + NetworkX JSON, so committed artifacts keep working; only incremental rebuilds are tied to graphify.

🤖 Generated with Claude Code