fix(exports): top-level-call consumer entries no longer masquerade as a named caller

[carlos-alm]

Problem

findCaller (src/domain/graph/builder/call-resolver.ts) falls back to the FILE node as a calls edge's source when a call is a bare top-level statement with no enclosing function/binding. findExternalConsumers (edges.ts) and its mirror in exports.ts discriminate consumerKind purely off edge kind ('calls' vs 'imports-type'), so this genuinely-real calls edge gets consumerKind: 'symbol' — but its name/file/line are the file node's own values (the file's basename, line 0), not a real caller symbol/call-site. codegraph exports/codegraph check output could therefore show something like consumer.ts (consumer.ts:0), which reads as if consumer.ts were itself a calling function.

This was an inherited characteristic of the existing discriminator design (present since #1973, explicitly called out as out-of-scope when #2189 fixed a related misclassification bug), flagged by Greptile on PR #2364 as worth addressing on its own.

Fix

Chose the least invasive of the three options the issue raised: added a third consumerKind value, 'topLevelCall', discriminated by additionally selecting the caller node's own kind column (not just the edge kind) — 'calls' edge + file-kind source → 'topLevelCall'; 'calls' edge + real source → 'symbol' (unchanged); 'imports-type' → 'file' (unchanged).

Did not pursue the other two options from the issue:

• Synthesizing a real call-site line for the bare top-level call would need a schema change (the edges table has no per-edge line column today) or a new synthetic-node scheme — a materially larger change than what this metadata-quality gap warrants.
• Documentation-only was the weakest option and doesn't actually fix the misleading CLI output.

Updated both renderers (presentation/check.ts, presentation/queries-cli/exports.ts) to present the new kind distinctly ("file.ts (top-level call)") rather than falling through to the generic name (file:line) format used for real named callers.

Closes #2365

Test plan

• Updated two existing regression tests (from checkNoDeletedExportsInUse consumer refs also conflate file-level imports-type with symbol-level calls #1973/exports' consumer discriminator (#1830) misclassifies top-level calls sourced from the file node #2189) whose fixtures are exactly this file-node-fallback scenario — they previously asserted consumerKind: 'symbol' for it, which is now 'topLevelCall'
• Added a new integration test asserting the new kind is distinct from a real named caller
• Added a new presentation-layer test asserting the CLI renders "file (top-level call)", not the file's own name as if it were a caller
• Verified consumerKind === 'symbol' assertions for genuinely real callers (main/testAdd calling add/multiply) are untouched
• Full vitest run suite (5283 passed, 328 files) after rebuilding the native addon (stale in the fresh worktree, unrelated to this TS-only change)
• tsc --noEmit, biome check clean
• TS-only change — confirmed via diff that no Rust files changed; this is query/presentation-layer code that reads from the already-built SQLite DB, not part of the dual-engine graph-building pipeline, so no Rust mirroring is needed

[greptile-apps]

Greptile Summary

The PR distinguishes bare top-level calls from named-symbol callers throughout export analysis and presentation.

• Adds the topLevelCall consumer classification to TypeScript query, advisory-reading, type, and rendering paths.
• Mirrors the classification in the native Rust deleted-export advisory writer.
• Adds regression coverage for native persistence, export analysis, checks, and CLI rendering.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains; the native advisory writer now mirrors the TypeScript classification, and the persisted value is preserved through the advisory reader and check renderer.

Important Files Changed

Filename	Overview
crates/codegraph-core/src/domain/graph/builder/stages/detect_changes.rs	The native advisory writer now selects the caller node kind and correctly persists topLevelCall for file-sourced call edges, resolving the previous thread.
src/db/repository/deleted-export-advisories.ts	The advisory reader preserves the newly persisted topLevelCall discriminator.
src/db/repository/edges.ts	Live external-consumer queries distinguish type imports, named callers, and file-sourced top-level calls.
src/domain/analysis/exports.ts	Export analysis applies the same three-way consumer classification used by the repository query.
src/presentation/check.ts	Check output renders top-level calls without presenting the file node as a named caller or fabricated call site.
src/presentation/queries-cli/exports.ts	Export CLI output renders the new consumer kind as a distinct top-level call.

_{Reviews (2): Last reviewed commit: "fix(native): deleted-export advisory wri..." | Re-trigger Greptile}

[github-actions]

Codegraph Impact Analysis

7 functions changed → 19 callers affected across 8 files

• getDeletedExportAdvisories in src/db/repository/deleted-export-advisories.ts:218 (3 transitive callers)
• findExternalConsumers in src/db/repository/edges.ts:220 (7 transitive callers)
• exportsFileImpl in src/domain/analysis/exports.ts:160 (3 transitive callers)
• buildSymbolResult in src/domain/analysis/exports.ts:230 (4 transitive callers)
• formatPredicateViolations in src/presentation/check.ts:64 (2 transitive callers)
• formatViolation in src/presentation/check.ts:79 (3 transitive callers)
• formatConsumer in src/presentation/queries-cli/exports.ts:21 (6 transitive callers)

[carlos-alm]

@greptileai please re-review — pushed the native-side advisory-writer fix you flagged.