CGIS Code Graph

Upstream subgraph of one FQN: everything that reaches it within ``depth`` hops. Follows every edge except containment — in practice callers, importers, subclasses, type references and DI dependents — within internal code, so this answers "what breaks if I change X?". The enclosing class or file and stdlib/third-party nodes are left out unless ``include_structure`` / ``include_external`` ask for them — the same view as the CLI's ``impact``. For what X depends on use ``cgis_trace_flow``; for only the members of a module or class, ``cgis_get_structure``; for a source-included brief to read before editing one symbol, ``cgis_context``. ``output_format="mermaid"`` (default) returns a diagram; ``"json"`` returns a joinable ``{root, nodes, edges, coverage}`` payload with real FQNs — letting an agent compute set differences (e.g. "which route handlers never reach ``verify_ownership``?") directly. ``coverage`` counts unresolved calls whose name matches a traversed function, method or class: callers that may be missing, named in ``top_unresolved``. It is an upper bound — a common name matches calls on unrelated objects, which the names make visible.

Reachability/authorization audit — which sources never reach a checkpoint. The headline use is **IDOR/authz coverage**: list every route handler that does NOT transitively reach an ownership check. Reachability follows behavioral edges (CALLS *and* FastAPI ``Depends()`` DEPENDS_ON), so a guard wired via DI counts. Select sources with ``from_type`` (a NodeType like ``ROUTE_HANDLER`` / ``API_ENDPOINT`` / ``FUNCTION``) and/or ``from_prefix`` (FQN prefix) — at least one is required. Returns JSON ``{target, covered, gaps}`` where each gap carries ``fqn``/``file``/``line``. Generalizes to validators, event tracking, or service-layer-boundary rules by pointing ``target`` at the required node. A selection that matches no source returns a ❌ message, not an empty ``{covered: [], gaps: []}`` that would read as a passing audit (#467).

Prompt-ready brief on one FQN: its source, class, direct callers and callees. Call this before editing a symbol, instead of reading its files. It follows calls only, one hop by default. Source is included when the file is found (see ``source_root``), and the domain when the graph was tagged with one. For a multi-hop subgraph over calls, imports, inheritance and references without source, use ``cgis_trace_flow`` (downstream) or ``cgis_analyze_impact`` (upstream). Returns an XML-tagged prompt — the focal node's source, its enclosing class, its architectural domain boundary, direct callers (upstream ripple) and callees (downstream dependencies) — meant to be injected into your context window in place of raw file dumps. Far more token-efficient than reading whole files, and structured so boundaries stay unambiguous. Use ``cgis_ingest`` first if the database does not exist. ``source_root`` locates source files on disk when the graph was ingested from a sub-directory (e.g. ``"src"`` after ``cgis ingest ./src``); it is safe to pass even when the stored paths already start with that segment (#228). When no candidate exists the ``<source>`` block degrades gracefully to "unavailable".

Report per-domain architectural drift against declared ideal patterns. Returns JSON: ``any_critical`` verdict, per-domain reports (each carrying a ``fit`` block — nearest alphabet template + residual + good/weak/none band), the observe-only quotient layer, and ``coverage`` (graph prefixes bound by no domain). Call after ``cgis_ingest`` to learn whether your edits pushed a domain past its drift tolerance. ``max_drift`` is now the default tolerance only for domains that omit ``drift_tolerance`` — it no longer caps domains that declare their own (see #170). ``profile``: when set, score only domains with this profile (plus profile-less ones). Use when your patterns.yaml mixes languages but the graph holds one language — avoids false EMPTY reports for other-language domains that would otherwise fail the gate. ``max_residual``: a domain whose nearest template is farther than this gets ``fit.band = "none"`` ("no template fits") — a grab-bag module or an alphabet gap, independent of drift tolerance (#177).

Classes nothing in production builds, extends or names — dead-code candidates. Finds classes that no test, type checker or linter flags, because each is still imported somewhere: a package re-export keeps a class importable long after its last real caller is gone. On one mid-sized backend this reported 43 of 1 789 classes, and the hand-written equivalent's findings were all real and all deleted. Two filters decide the answer. **Tests are not users** — a class built only by its own test is exactly the shape being hunted. **A re-export is not a use** — ``IMPORTS_SYMBOL`` does not count, or nothing is ever reported. What counts is construction (``CALLS``), inheritance (``EXTENDS``) and being named (``REFERENCES`` — an annotation, or a class handed to a framework); the last keeps abstract ports and Protocols off the list. ``prefix`` narrows to one package on a dot boundary. ``include_tests`` counts test code as a user, turning the report into "unreachable from anywhere". Machine-generated classes are **hidden by default**, and ``include_generated`` puts them back. The query is right about them — nothing constructs a betterproto stub — but nobody hand-deletes one either, so they are noise rather than a finding. Measured on owner-api at b7d02fe6, five of six reported orphans were generated entities and the sixth a nested pydantic ``Config``: the unfiltered report had no actionable row in it (#432). Returns JSON ``{orphans, considered, test_sources, generated_excluded}``; each orphan carries ``fqn``/``file``/``line``. **A listing is a candidate for deletion, not a proof** — a class named only inside a decorator (#429) or arriving through a star import is invisible here, so the sweep errs towards reporting a live class rather than hiding a dead one. ``test_sources: 0`` in a repository that has tests means the graph predates the ``is_test`` column: re-ingest. ``generated_excluded`` counts every generated class left out of the population under the same ``prefix``, refer…

Resolve a partial symbol name to candidate FQNs (substring match, ranked). Call this BEFORE ``cgis_trace_flow`` / ``cgis_analyze_impact`` / ``cgis_get_structure`` when you know a short name (e.g. ``get_reservation_prices``) but not its full FQN — it removes the read-the-file-first guesswork. Returns JSON ``[{fqn, name, type, file, line}]`` ranked exact > prefix > substring. ``kind`` filters by node type (FUNCTION / METHOD / CLASS / …); ``fqn_prefix`` scopes the search.

Report the motif census across the repository's structural tiers. Coarsens the graph along its own structure — symbol, class, module, then directory levels trimmed from the leaf end — and measures the 13-triad census at every rung. Returns JSON: one entry per layer (IMPORTS, CALLS) with the full per-rung curve (groups, triads, entropy in bits, dominant motif, tangle ratio) and the fit. ``verdict`` is the sign of ``slope`` (entropy bits per halving of the group count) outside a ``2 * std_error`` dead-band: ``hierarchical`` means coarsening ADDS motif diversity, ``flat`` means it destroys it, ``scale_invariant`` means the mix is the same at every scale, and ``no_signal`` means fewer than three rungs carried enough triads to fit. Read the curve, not just the verdict — the fit is a lossy summary of a non-linear curve. Observe-only: this tool enforces nothing and no gate reads it. Call after ``cgis_ingest``.

Members of a module or class — or, for a package prefix, the modules it holds. Follows containment (CONTAINS/DECLARES) only, so no call or import appears. A package is not a node in the graph (#487), so its row and the edges to its modules are synthesized for the answer and marked with a virtual file path. For how the code connects use ``cgis_trace_flow`` (what it depends on) or ``cgis_analyze_impact`` (what depends on it). Matches the CLI ``structure`` command. ``output_format="mermaid"`` (default) returns a diagram of the hierarchy rooted at the given FQN; ``"json"`` returns the joinable ``{root, nodes, edges}`` payload with real FQNs.

Scan a local directory, extract all symbols, resolve links, and build the graph DB. Use this to initialise or refresh the code knowledge graph for a project. Node FQNs are normalised relative to the workspace root so the graph is portable across machines. ``db_path`` must name a database — it has to end in ``.db``, ``.sqlite`` or ``.sqlite3``, live in a directory that already exists, and not point at an existing file that is not a SQLite database. cgis will not create parent directories. By default the ingest is **incremental**: only changed/new files are re-scanned, and the summary reports both what changed this run and the whole-graph total. When a change alters what other files resolve against — a renamed, removed or added symbol, a deleted or new file, a changed base class or re-export — the incremental run rebuilds the whole graph itself, so edges in unchanged files never point at symbols that no longer exist. Set ``full_rebuild=True`` to force a re-scan of every file from scratch.

Propose a starter patterns.yaml from the measured graph (read-only). Returns the YAML text — save it yourself (e.g. to patterns.yaml), review the proposed labels, then run ``cgis_drift`` with it. Tolerances are the measured scores plus ``margin``: a baseline to ratchet down, not a verdict. No files are written; the caller decides where to persist the output.

Whole-graph architectural metrics — coupling bottlenecks, God classes, PageRank. Returns JSON ``{bottlenecks, god_classes, critical}`` computed with vectorized DuckDB aggregations over the whole graph (fan-in/fan-out coupling, declared-member counts, PageRank) — the global "what are the hotspots?" view that complements the node-local trace/impact/context tools. Requires the optional ``duckdb`` extra; an unavailable dependency is reported as a normal ❌ message. ``exclude`` drops any node whose FQN contains one of the given dot-segments (e.g. ``["tests"]`` removes both ``tests.*`` and ``domains.*.tests.*``) so test/vendor scaffolding stays out of the rankings. ``scope`` is its complement: it keeps only nodes under one of the given dot-prefixes, anchored and cut on a dot boundary, so ``["domains.reservation"]`` is that subtree and not ``domains.reservation_archive``. Use it for a per-domain review. The two compose, and they differ where it matters for PageRank — ``exclude`` removes nodes from the propagation graph, ``scope`` filters the rows and lets rank propagate over the whole graph, so a scoped run reports how central the subtree is *globally*. Coupling in-degree likewise keeps counting callers from outside the scope, which is the ripple a domain review is after (#239).

Where to start in a graph you know nothing about: sizes and a package map. Call this first in an unfamiliar repository — every other tool needs a name, and this is the one that hands you some. Returns JSON: symbol counts by type, file and edge totals, the unresolved-edge ratio, and the largest packages with production and tests listed separately. Each ``prefix`` goes straight into ``cgis_get_structure`` (the modules it holds), ``cgis_find_symbol`` (``fqn_prefix``) or ``cgis_metrics`` (``scope``). Listings are capped; ``packages_omitted`` appears when rows were cut. Entry points are deliberately not reported — "nothing calls it" is not one on a framework codebase, where most handlers have no incoming call edge.

Suggest sub-package boundaries for a package from its dependency communities. Returns JSON: modularity_q, divergence, direction (under/over/matched), verdict (split/consolidate/aligned/leave/borderline/no_signal), the detected communities (id + member files), the cross-community bridge edges (cost of splitting), and the thresholds used. Default layer is IMPORTS; set ``with_calls`` for the combined import+call graph. Run ``cgis_ingest`` first. A mis-rooted graph (import targets resolve to no internal file) returns ``no_signal`` with a diagnostic note rather than a silent clean verdict.

Downstream subgraph of one FQN: everything it reaches within ``depth`` hops. Follows every edge except containment — in practice calls, imports, inheritance, DI dependencies and references — between internal code, so this answers "what does X depend on?". Containment and stdlib/third-party nodes are left out unless ``include_structure`` / ``include_external`` ask for them (external covers stdlib, third-party and unresolved call targets) — the same view as the CLI's ``trace``. For what depends on X use ``cgis_analyze_impact``; for only the members of a module or class, ``cgis_get_structure``; for a source-included brief to read before editing one symbol, ``cgis_context``. ``output_format="mermaid"`` (default) returns a human-readable diagram; ``"json"`` returns a joinable ``{root, nodes, edges, coverage}`` payload with real FQNs (not display hashes) for agent/CI use. ``coverage`` counts the calls the traversed functions make that resolved to nothing, and ``top_unresolved`` names the most frequent. Read the names, not only the ratio: in Python most are methods on untyped locals (``logger.info``, ``items.append``), which cut nothing short. Use ``cgis_ingest`` first if the database does not exist yet.

Report graph integrity as JSON: edge resolution stats + health verdict. Check this before trusting ``cgis_analyze_impact`` output — a high unresolved ratio means callers are missing from the graph.