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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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Fix Node.js CLI tools crashing inside Docker containers when host-installed node_modules require a newer Node version than the container provides. Use when: (1) "SyntaxError: Invalid regular expression flags" with /v flag in string-width or similar packages, (2) node_modules installed on host with Node 20+ but container has Node 18, (3) `npm install` with file: protocol creates symlinks that break inside Docker, (4) pnpm workspace packages become broken symlinks in containers. Covers version detection, Node binary mounting, and npm install strategies for cross-version compatibility.

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Fix intermittent `{:no_translation, :unicode, :latin1}` crashes in Elixir escript daemons that use length-prefixed framed IPC on stdin/stdout. Use when: (1) daemon worker crashes only on some input files, usually ones with non-ASCII bytes (kanji, cyrillic, emoji); (2) error surfaces as `Protocol error` from daemon's error branch or as garbled frame-length bytes seen by the orchestrator/client side; (3) standalone one-shot mode works fine on the same input but multi-request daemon mode fails; (4) `IO.binread(:stdio, N)` returns `{:error, {:no_translation, :unicode, :latin1}}` despite the "bin" prefix suggesting it should be encoding-agnostic. Root cause is the escript default `:standard_io` encoding — it's `:unicode`, and `IO.binread` still routes through the io_server, which translates bytes to codepoints and errors when raw binary frames contain invalid UTF-8 sequences.

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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 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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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 drifting into "I think that..." without evidence, (4) about to report "готово", (5) copying a pattern from one place to another, (6) task took >2× expected time. Embeds scientific method (explicit hypotheses + falsifiability + prediction-first + alternatives) as substrate for premise-level reflection, not as ceremony.

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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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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.

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Fix Elixir/Erlang AST processing bugs in Grafema beam-analyzer. Use when: (1) Elixir parser returns MODULE node but 0 functions/calls — body nesting issue, (2) Erlang parser crashes with "cannot convert list to string" on OTP 26+ — location format changed from integer to keyword list, (3) pipe operator |> creates spurious CALL nodes instead of desugared function calls — clause ordering bug, (4) multi-module .ex files return only the first module — missing __block__ handler, (5) installing Erlang/Elixir on macOS with outdated Xcode/Clang.

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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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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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Fix Playwright automation failures against code-server (VS Code in browser). Use when: (1) trust dialog blocks all clicks — "monaco-dialog-modal-block intercepts pointer events", (2) button:has-text() finds wrong buttons behind modal dialog, (3) keyboard shortcuts don't work — Meta vs Control inconsistency, (4) VS Code extension activity bar icon not found by aria-label, (5) panels show placeholder text despite extension being "Connected". Covers trust dialog dismissal, keyboard shortcut hybrid mode, extension panel selectors, and database connection verification for Grafema extension.

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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.

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Fires after fixing any non-trivial bug or regression. Asks: could the graph have caught this as a guarantee? Pairs with reflection-in-and-on-action — picks up after "earliest catchable signal" and asks the next question: was that signal expressible in graph? Triggers: (1) after any non-trivial bug fix is verified working, (2) after a regression report (something used to work, broke), (3) during step 6 (knowledge extraction) of the workflow, (4) when reflection-on-action surfaces a "would have been catchable" signal. Outcome is a triage decision (graph-reachable? rule expressible? rule sound?) and either a draft Linear issue + guarantee proposal, or a recorded "graph capability gap" note. Never auto-creates guarantees.

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Systematic methodology for achieving 100% backward dataflow reachability in a new language. Create gauntlet fixture, write trace, diagnose gaps, fix analyzer/algorithm, iterate to 100%. Language-agnostic process. Use when: (1) adding a new language to Grafema, (2) auditing dataflow coverage for existing language, (3) user says "/dataflow-gauntlet".

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Fix docker exec hanging when starting background processes (servers, daemons) inside containers. Use when: (1) docker exec never returns despite using & or nohup, (2) background server started in container causes docker exec to hang indefinitely, (3) env_startup_command in SWE-bench or similar frameworks times out, (4) setsid/disown needed for proper process detachment in Docker. Root cause: docker exec tracks ALL processes in the exec session, not just the top-level PID.

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Extract knowledge (decisions, facts, session metadata) from the current Claude Code session into the Grafema Knowledge Base. Run after completing a task or at any point when substantive knowledge was produced. Follows runbook _ai/runbooks/02-claude-sessions.md.

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Cyclical dogfooding loop: test AI-AGENT-STORIES.md against the live graph, discover new stories, analyze gaps, fix root causes, re-test, write report. Use when: (1) user says "/gap-loop", (2) periodic dogfooding session, (3) after a release or major feature to re-validate stories, (4) before sprint planning to prioritize product gaps.

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How to write a Grafema batch-mode plugin that reads the graph and filesystem, then writes new edges/nodes directly to RFDB. Use when: (1) need to add project-specific edges that generic analyzers can't produce, (2) need to read config files (JSON/YAML) and trace values into code, (3) implementing framework-specific resolvers (Django settings, Express routes, pipeline configs). Covers: grafema.config.yaml plugin config, RFDB field naming (src/dst NOT source/target), addEdges/addNodes API, RFDBServerBackend connection pattern.

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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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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.

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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 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 manually via pnpm snapshots:update when needed.

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Fix silent failures when parsing Grafema semantic IDs that are in URI format instead of legacy arrow format. Use when: (1) code splits semantic IDs by "->" but gets the whole string back because IDs are grafema:// URIs, (2) file path extraction from semantic IDs returns empty or wrong values, (3) derived edges (DEPENDS_ON, etc.) produce 0 results despite source edges existing, (4) any code that processes semantic IDs after the analysis pipeline's to_uri_format() has run. The grafema:// URI format uses # fragments with percent-encoded characters instead of -> separators.

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