CFG & Taint Analysis with GitNexus

Expert knowledge for the opt-in --pdg program-analysis subsystem: control-flow graphs, reaching definitions, and intra- + inter-procedural taint. Read this before touching gitnexus/src/core/ingestion/cfg/** or gitnexus/src/core/ingestion/taint/**, or when explaining a finding.

When to Use

• "How does the taint engine work / why is this flow (not) reported?"
• Adding a source, sink, or sanitizer to the model.
• Extending or reviewing the CFG / reaching-defs / taint / summary code.
• Understanding the explain MCP tool's findings (intra- vs inter-procedural).
• Debugging a false positive or false negative in --pdg output.

The layered substrate (build order)

Taint runs on the graph, not beside it. Each layer is opt-in behind --pdg and a default analyze run is byte-identical (the golden parity gate is the hard floor for every change here).

L1  CFG            per-function basic blocks + control-flow edges   (M1 #2081)
L2  REACHING_DEF   GEN/KILL def→use data dependence (pure solver)   (M2 #2082)
L3  Taint (intra)  source→sink over RD facts, minus sanitizers      (M3 #2083)
L4  Taint (inter)  per-function summaries composed over CALLS       (M4 #2084)

• Worker-built, main-thread-solved. The parse worker builds each function's CFG + harvests def/use + call-site facts onto ParsedFile.cfgSideChannel (plain, structured-clone-safe data — never AST nodes). The main thread runs the pure solvers. NEVER re-parse on the main thread (re-introduces the #1983 OOM).
• In-phase emit (KTD1). L1–L4-harvest all run INSIDE the scope-resolution pdg window (scope-resolution/pipeline/run.ts, gated input.pdg === true), because the disk-backed ParsedFile store is cleared when that phase ends — a standalone post-mro phase would read empty data. The cross-function fixpoint (L4) is the exception: it runs in its OWN registered phase (taintSummaries) AFTER scope-resolution, because it needs the COMPLETE call graph, and consumes small plain summary data threaded out via ScopeResolutionOutput.
• Pure-solver contract. computeReachingDefs, computeTaintFlows, harvestFunctionSummary, and solveInterprocTaint are pure and deterministic (no graph, no I/O, no logger; sorted outputs). Snapshot tests and content-derived edge ids depend on it.

Intra-procedural taint (L3)

Forward reachability over RD facts from matched sources to matched sinks, killed by sanitizers. Key design points worth internalizing:

• Occurrence-tagged sites. A flat per-arg binding set cannot tell exec(escape(x)) (safe) from exec(x) (finding); the harvest records nested call structure (SiteRecord.parent/via-tags) so sanitizer interposition is precise.
• Kind-set sanitizer model. A taint carries a set of neutralized SinkKinds; a sink fires unless its kind is in the set. So escape(req.body) suppresses res.send (xss) but STILL fires db.query (sql) — a kind-blind kill would be a suppressed live injection (the forbidden FN direction). path.basename(t) neutralizes path-traversal only, not command-injection.
• Statement-level finding identity. NOT block-pair (block conflation drops distinct findings; exec(req.body, req.query) is two findings).
• Persisted as TAINTED edges (BasicBlock→BasicBlock); the path rides the reason column via the shared versioned codec (taint/path-codec.ts).

Interprocedural taint (L4) — the functional/summary method

The production approach (Sharir-Pnueli 1981; the same shape as Meta's Pysa and Mariana Trench, and FB Infer) — NOT full IFDS tabulation. Each function is reduced to a compact summary, and summaries are composed over the already- resolved CALLS graph.

Summary shape (taint/summary-model.ts, whole-parameter granularity):

The fixpoint (taint/interproc-solver.ts): the unit is (function, parameter, source). Seed from source→callee-arg, propagate via param→callee-arg, fire a finding when a tainted param meets param→sink.

• Cycle-safe by monotonicity. The tainted-set is monotone over a finite lattice (fn × param × source), so the worklist converges — a recursive call just re-proposes an already-visited entry. SCC condensation would only refine processing order; correctness/termination don't require it.
• Source-discriminated state (load-bearing). Key the state by the SOURCE too. Keying only by (fn, param) collapses multi-source flows: a sink param tainted by source A is marked visited and a later flow from source B is dropped before firing — the recurring multi-source bug class. (Bit M3; bit M4 U9.)
• Name-based call join. Match a summary's call-arg edge to a CALLS edge by CALLEE NAME, not call-site line — line-base parity (CFG 1-based vs reference site) is fragile; the callee identity is exact and context-insensitivity taints the callee's param identically at every call site.
• Persisted as TAINT_PATH edges (Function→Function), function-level hop chain in reason via the same codec; confidence < the intra-procedural 1.0.

Context-insensitivity is the accepted trade-off at this tier: one summary per function, return/call-site merging accepted (security-conservative). Expect some FP from merging; the bigger FN sources are unmodeled features (below).

Known false-negative classes (documented, deferred)

The largest is closures/callbacks (arr.forEach(() => sink(y))) — taint into a callback is dropped without per-library models (true of CodeQL's JS libs too). Also deferred: field/property flows (obj.x = taint; sink(obj.y)), field-sensitive access paths, guard-style sanitizers, implicit/control-dependence flows, promise/async-await threading, and destructured/rest params before a tainted simple param (the summary port index is the binding ordinal, not the formal arg position — needs a formal-param index threaded from the worker BindingEntry). The interprocedural join is also context-insensitive: when one caller invokes two distinct same-named callees, a flow into one over-attributes to both (sound — over-report, never a missed flow). Absence of a finding is NOT proof of safety.

GitNexus-specific gotchas

• Function↔CFG join. FunctionCfg.functionStartLine is 1-based; Function/ Method node startLine is 0-based — join at startLine - 1. Function nodes have no column, so same-line functions ({a:()=>x(), b:()=>y()}) are ambiguous → drop (the summary driver counts unresolved) rather than cross-wire.
• No rel-property index (S1). Kuzu has no secondary index on relationship properties, and unanchored [:TAINTED*]/[:TAINT_PATH*] queries explode. TAINT_PATH is therefore MATERIALIZED + anchored at analyze time, never traversed live; explain reads it source-anchored + LIMIT-guarded.
• explain is the only discovery surface. TAINTED/TAINT_PATH are deliberately OUT of VALID_RELATION_TYPES (impact's allow-list) and the web schema (pinned in security.test.ts). explain enumerates both layers (cross-function findings carry interprocedural: true).
• One shared codec. Both the emit path and explain import taint/path-codec.ts. Two hand-rolled copies of a wire format drift — never fork it. New metadata extends the format WITHIN the version when writer + reader ship together.
• Cache versioning. A worker-harvest shape change bumps the parse-cache pdg NAMESPACE (pdg:N), NOT SCHEMA_BUMP (which cold-invalidates every user). Persisted-graph/config changes ride RepoMeta.pdg's key-union mismatch → full writeback. Model content rides taintModelVersion.

Adding a source / sink / sanitizer

Taint models cover four SupportedLanguages ids across three files: TypeScript and JavaScript use taint/typescript-model.ts, Python uses taint/python-model.ts, and Java uses taint/java-model.ts. Edit the model for the language you are targeting. The explicit registerBuiltinTaintModels seam in typescript-model.ts registers all four; it is not an import side effect.

The spec is hashable data (no functions). A sanitizer's neutralizes lists the EXACT sink kinds it defends — never a blanket kill. Add a fixture + assert the finding (or its absence) in test/unit/taint/. TypeScript and JavaScript use the real-source harness test/helpers/ts-cfg-harness.ts; Python and Java model matches are covered by python-model-match.test.ts and java-model-match.test.ts. The end-to-end proof is test/integration/cfg/.

Validation checklist for any --pdg change

1. tsc clean (schema additions are exhaustiveness-checked; watch the
   api.ts getNodeQuery runtime read-path if a node label is added).
2. Targeted vitest by directory (test/unit/taint, test/unit/cfg,
   test/integration/cfg) — verify by ISOLATION, not full-suite exit
   (known load-flakes). `node scripts/build.js` before worker/integration runs.
3. Flag-off golden byte-identical (pipeline-graph-golden.test.ts).
4. bench/cfg/measure.mjs --check (no fingerprint drift / budget regression).
5. detect_changes() before commit; impact({direction:'upstream'}) before
   editing shared symbols (KnowledgeGraph, RepoMeta, RelationshipType, codec).

Prior art (for deeper design questions)

Sharir & Pnueli 1981 (functional approach); Reps-Horwitz-Sagiv IFDS (POPL 1995); FlowDroid/StubDroid (access-path summaries); Pysa & Mariana Trench (TITO / propagations, parallel SCC fixpoint); CodeQL Models-as-Data (the richest port notation, incl. callback ports); Infer (content-keyed incremental summaries).