Data & Analytics

Analyze codebases using a graph database instead of reading source files. Use when understanding code architecture, finding functions or call patterns, tracing data flow, checking dependencies, or answering "where is X used?" questions. Grafema builds a queryable code graph from static analysis — prefer querying the graph over reading files manually.

Verify which process actually owns a TCP port before assuming your fresh restart succeeded. Use when: (1) you killed an old server and started a new one but behaviour matches the OLD code/data, (2) `pkill -f pattern` returned 0 but old behaviour persists, (3) you embedded a new asset/binary but the served version is stale, (4) any "I just restarted X but I'm getting old results" situation. `pkill -f` matches against the process command line — if the live old process was started with `--port 0...

Verify task completion by demonstrating real value: run the new code on real data, show visible results, find gaps between plan and reality. Not about tests/builds — about proving the feature WORKS end-to-end.

Activate theoretical foundations context for discussions about Grafema's formal underpinnings, multi-language strategy, cognitive science, and abstract architecture. Use when: (1) discussing formal languages, type theory, abstract interpretation, (2) planning multi-language support, (3) designing metrics or benchmarks, (4) reasoning about completeness and soundness of analysis, (5) positioning Grafema academically.

SWE-bench pipeline for A/B testing Grafema with Claude Code. Use when: (1) running SWE-bench experiments, (2) comparing baseline vs grafema conditions, (3) evaluating results, (4) debugging container issues.

Build all packages, reinstall VS Code extension, commit and push. Use when: user says "ship", or wants to build+install+commit+push in one go.

Force `rust-embed` to re-embed assets from `$GRAFEMA_UI_DIST` (or any env-driven path) when cargo's incremental compilation skips the macro re-expansion. Use when: (1) you rebuilt the GUI bundle but the rust-server binary still serves the OLD bundle, (2) `cargo build --release` finishes in seconds (incremental hit) and `strings target/release/binary | grep <new-hash>` finds nothing, (3) any rust-embed pipeline where assets live outside the cargo source tree and are picked up via env var or sy...

Speed up Rust development iteration when `cargo build --release` takes 10+ minutes even for one-line edits. Use when: (1) every release rebuild takes minutes despite tiny edits, (2) Cargo.toml has `lto = "fat"` and/or `codegen-units = 1` in `[profile.release]`, (3) you want a production- shaped build for testing without paying the LTO cost on every iteration, (4) you suspect cargo is re-linking the whole binary instead of doing incremental work, (5) developing rfdb/grafema-orchestrator/large ...

RFDB server becomes unresponsive (60s+ timeouts) during enricher addEdges write storms. Use when: (1) RFDB CPU spikes to 60-90% after addEdges calls; (2) subsequent reads time out at 60s; (3) server stays catatonic for 5-15 min after a write storm; (4) Tokio main thread parked (write-lock contention). Root cause: add_edges() calls maybe_auto_flush() which has a memory-pressure path that fires on NODE count — not edge count — and holds the exclusive write lock during disk I/O. Fix: separate ma...

Fix RFDB V2 graph data silently not persisting to disk after analysis. Use when: (1) rfdb-server reports "0 nodes, 0 edges" on restart despite successful analysis, (2) segment directories exist but are empty (no .bin files), (3) manifest_index.json shows total_nodes: 0 despite analysis logging 70k+ nodes, (4) Docker builds produce empty graph databases, (5) --clear flag used before analyze command. Root cause: GraphEngineV2::clear() replaces the store with MultiShardStore::ephemeral() which h...

Diagnose and fix RFDB data disappearing after compaction, where rfdb-server reports a tiny node count (e.g. "15 nodes") on startup despite manifest_index.json showing hundreds of thousands of nodes and segment files existing on disk. Use when: (1) rfdb-server logs "Default database: N nodes" with N orders of magnitude smaller than recent analysis output, (2) /api/stats returns only the most recent commit's nodes, (3) the issue appears AFTER a compaction event (manifest with l1_node_segments p...

Fix silent incorrect results in RFDB Datalog queries that share a variable between two edge atoms on opposite ends (e.g. self-join patterns like `edge(M, C, "T1"), edge(C, M, "T2")`). Use when: (1) a Datalog rule returns rows that look structurally wrong (e.g. a self-loop rule reports hits but pinning M to each reported id refutes the edge existence), (2) Cypher `MATCH (m)-[:R1]->(c)-[:R2]->(m)` returns the same bogus rows (engine-level bug, not Datalog-specific), (3) results change when you ...

Fix nodes silently disappearing from RFDB when an enricher or post-resolution pass writes new nodes via BatchHandle. Use when: (1) writing a TypeScript enricher that should ADD nodes/edges to existing files, (2) after calling `client.createBatch()` + `batch.addNode({file: 'X', ...})` + `batch.commit()` the original nodes in file X have vanished, (3) tests that load a graph fixture, run an enricher, then query original nodes get empty results, (4) a verification step shows expected nodes pre-e...

Continuous self-reflection routine combining Schön (reflection-in-action / reflection-on-action) and Mezirow (content / process / premise) levels, anchored on KAMI values (val-002 глубина, val-007 честность перед собой, принцип 1 правда, принцип 2 нулевая толерантность к бреду). Triggers FIRE DURING THE TURN, not at end. Use when: (1) about to make a 2nd+ patch attempt at the same problem, (2) user pushes back with "стоп / нет / опять / так, ещё раз / не то / пиздёж", (3) noticing self drifti...

Run automated QA checks on Grafema VS Code extension via Playwright + MCP cross-validation. Use when: (1) user says "/qa" to start or resume QA session, (2) user wants to validate extension panels against graph data, (3) user wants to re-check previously found bugs after a fix, (4) user wants to run a custom QA task. Requires Docker code-server running.

Decide what to PERSIST in your data structures (graph nodes, DB tables, cache layouts) based on the QUERIES you must answer, not the DEFINITIONS that justify the data. Definitions tell you logical identity; storage strategy is independent. Materializing every definitional component leads to O(N×M) blow-ups that masquerade as memory leaks. Use when: (1) designing a new graph-node type, edge type, DB table, or cache layout; (2) about to name a `subgraph` / `comprises` / `members` / `contains` c...

Fix missing theorem proof terms when analyzing Lean 4 environments via importModules. Use when: (1) ConstantInfo.value? returns none for theorems despite TheoremVal.value being Expr, (2) building code graph / dependency extractor for Lean 4 and getting 0 proof dependency edges, (3) Lean 4.30+ project where theorem proofs appear missing from loaded environment, (4) analyzing Mathlib or any Lean 4 project and proof terms are empty. Root cause: breaking change in Lean 4.30 — value? treats theore...

Fix scattered/torn regions in hex-grid simulated annealing layouts that use "competitive flood-fill" (one tile per region per outer iteration). Use when: (1) regions of >20 tiles end up dispersed instead of forming compact blobs, (2) maxDist/sqrt(N) dispersion ratio is 10×+ worse than the ideal compact blob, (3) tiles assigned to one region show up in multiple disconnected fragments across the layout, (4) the visualization has a "trypophobia ring" pattern at the perimeter where some regions s...

Compute a unified outer hull around a group of hex tiles that includes multiple disconnected sub-clusters separated by 1-tile gaps. Use when: (1) rendering nested hierarchy hulls (e.g. "package" hull wrapping multiple "sub-region" hex islands), (2) the naive boundary trace outlines each island separately instead of as one bag, (3) flood-fill from outside walks THROUGH the 1-hex gaps and marks them exterior, (4) heuristic "non-adjacent same-group neighbours" over-fills L-shape concavities, (5)...

Design guide + benchmarked pitfalls for building Monte-Carlo / Simulated Annealing refinement layers on top of greedy hex-grid layouts for code visualization (packages/gui/src/store/hexLayout.ts, sandbox/hex-sandbox, future Rust ports). Use when: (1) planning to add MC/SA on top of an existing hex-grid pack, (2) deciding whether a simpler SA would match a hierarchical MC with force-directed + chain drag, (3) budgeting wall-clock for million-node cold-start, (4) debugging "blob turns Swiss-che...

Diagnose React + Three.js (or any browser canvas) frame stutter by capturing a CDP CPU profile via Playwright instead of guessing from `[perf]` console logs. Use when: (1) frame time is bad but `[perf]` instrumentation doesn't pinpoint the offender, (2) you've spent more than ~30 minutes "fixing" suspects without measuring, (3) hot paths involve animation systems, allocation bursts, or invisible scene-graph traversal, (4) you need self-time per function with line numbers, not aggregate "rende...

Fix GraphSnapshot tests blocking CI on every feature PR. Use when: (1) every PR fails CI with "Snapshot mismatch" despite correct behavior, (2) fixing snapshots requires build → regen → commit → wait CI cycle per PR, (3) snapshot test in test/unit/*.test.js glob breaks on any intentional change, (4) pre-push hook runs pnpm build + snapshots:update on every push (2-3min overhead). Solution: move GraphSnapshot.test.js to test/unit/snapshots/ so it's excluded from the *.test.js glob. Run manuall...

Grafema release procedure for publishing new versions to npm. Covers happy path, pitfalls, rfdb binary lifecycle, and rollback. Use when user says "release", "publish", "bump version".

Pattern for adding derived edge types in the Grafema Rust orchestrator (main.rs). Use when: (1) need to create new graph edges derived from existing edges (e.g., MODULE-level DEPENDS_ON from IMPORTS_FROM), (2) Datalog joins on large edge sets time out, (3) adding enrichment steps that combine data from multiple resolver outputs, (4) need to understand how resolver outputs flow through the orchestrator pipeline.