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Fix stale Haskell analyzer binaries silently being used by the orchestrator even after a successful rebuild. Use when: (1) modified `packages/js-analyzer/` or other Haskell analyzer source, ran `scripts/build-native.sh ... cabal install`, but a subsequent `grafema analyze` shows old behavior (missing new edges, no new node types, etc.), (2) `~/.cabal/bin/grafema-analyzer` has fresh timestamp but `grafema analyze` produces output as if the change didn't happen, (3) a test verifying new analyzer output passes locally in unit tests but fails in end-to-end runs that go through the orchestrator. Root cause: the Rust orchestrator's `resolve_binary` checks `~/.grafema/bin/<name>` BEFORE `~/.cabal/bin/<name>`, so any stale copy that was once installed there (possibly months ago) shadows the fresh `cabal install` output.

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Fix silent metadata issues in RFDB node storage. Covers two traps: (1) metadata flattening — nested metadata fields become top-level after serialization, so node.metadata.field is undefined but node.field works. (2) reserved keys — fields named "type", "id", "name", "file", "exported" are silently stripped from metadata by _parseNode() to prevent overwriting top-level node fields.

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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".

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Fix node query issues in Grafema tests when nodes have numeric IDs instead of human-readable IDs, or when `type` field is undefined. Use when: (1) queryNodes returns nodes with numeric IDs like "52710336597754872375318185843222727675" instead of semantic IDs like "net:request#__network__", (2) node.type is undefined but node.nodeType has a value, (3) metadata is a JSON string instead of parsed object, (4) tests fail with "Cannot read property 'length' of undefined" after queryNodes. Covers RFDBServerBackend vs RFDBClient distinction and async generator handling.

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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-cheese" or "folders stop nucleating" during MC refinement, (5) choosing between folder cohesion and raw Σ-link-length as cost function. Contains four hard-won, quantified lessons and anti-patterns that would take a full day of experiments to rediscover.

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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) axial-only opposite-pair filling misses non-axial bridges between islands. Solution: morphological close (dilate + erode) on the hex grid — fills exactly the interior 1-hex gaps without affecting exterior corners, then trace boundary on the closed shape.

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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 spill into a perimeter spiral, (5) an overflow spiral fallback exists in the layout code and frequently kicks in for large regions, (6) bigger regions look worse than smaller ones (small regions stay compact, big ones shred). Root cause: interleaved competitive flood-fill (round-robin one tile at a time across all regions) lets large regions get boxed in by neighbors before they finish growing — the unfilled remainder is dumped into the overflow spiral at the perimeter, far from the seed. Fix: replace with sequential region-by-region BFS — process regions in size-descending order, fully claim each region's N contiguous tiles before moving to the next.

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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 populated and node_segments: []), (4) subsequent commits dropped L1 references. Root cause: ManifestStore::create_manifest() initializes l1_node_segments/l1_edge_segments to Vec::new() instead of cloning from current manifest, so any commit AFTER compaction silently orphans all L1 data even though segment .seg files still exist on disk. Compaction injects L1 fields explicitly after create_manifest, but regular commits do not.

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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 has path: None, causing all flush operations to write to in-memory buffers only.

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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 maybe_auto_flush_edges() uses byte-limit only.

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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 Rust binaries where full LTO is enabled for shipped builds. Adds a `fast` profile that inherits release but disables LTO, raises codegen-units, enables incremental compilation — first build still slow because it populates a fresh `target/fast/` dep cache, but every subsequent rebuild drops from ~13 min to ~13 s (≈60×).

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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 symlink. Cargo only re-runs the proc macro when the rust file declaring `#[derive(RustEmbed)]` changes — env var changes alone don't trigger it.

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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.

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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.

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