fix: replace fixed-depth directory-proximity check with symmetric distance (docs check acknowledged)

computeConfidence (and its Rust mirror compute_confidence) scored call-edge
resolution confidence using a fixed-depth check: same-directory, or
dirname(dirname(caller)) === dirname(dirname(target)) for a "sibling
directory" tier. That equality only holds when both files sit at the same
depth, so a file in a subdirectory calling a method on a class declared in
its direct parent directory (e.g. graph/algorithms/bfs.ts calling a method
on the CodeGraph class in graph/model.ts) was scored as maximally distant
(0.3) even though the receiver's type had already been correctly resolved
via typeMap (from the parameter's `graph: CodeGraph` type annotation). That
score fell below the 0.5 threshold used by resolveViaTypedMethod, silently
dropping the call edge.

Replaced both fixed-depth checks with a symmetric, depth-independent
directory-tree distance (hops to the nearest common ancestor), preserving
the existing same-directory (0.7) and sibling (0.5) tiers exactly and adding
a new tier for direct parent/child directory nesting (0.6).

Verified via the resolution-benchmark suite before/after the fix: all 42
language fixtures produce byte-identical precision/recall/TP/FP/FN numbers
(aggregate recall 63.8%, 355/556 edges) — no regression.

Fixes #1769

Impact: 3 functions changed, 26 affected

Author: carlos-alm

crates/codegraph-core/src/domain/graph/resolve.rs

@@ -247,8 +247,42 @@ fn resolve_import_path_inner(
     relativize_to_root(&resolved.display().to_string().replace('\\', "/"), root_dir)
 }
 
+/// All ancestor directories of `dir`, starting with `dir` itself, walking up to the root.
+fn ancestor_chain(dir: &str) -> Vec<String> {
+    let mut chain = vec![dir.to_string()];
+    let mut cur = dir.to_string();
+    while let Some(parent) = Path::new(&cur).parent() {
+        let parent_str = parent.display().to_string();
+        chain.push(parent_str.clone());
+        cur = parent_str;
+    }
+    chain
+}
+
+/// Directory-tree distance between two directories: hops up from `a` to the
+/// nearest ancestor shared with `b`, plus hops down from there to `b`.
+///
+/// Symmetric and depth-independent — unlike a fixed-depth equality check
+/// (e.g. comparing the parent-of-parent of `a` to the parent-of-parent of
+/// `b`, as `compute_confidence` used to), this correctly scores both sibling
+/// directories (common parent) and direct ancestor/descendant directories
+/// (one nested inside the other) regardless of how deep either path is. The
+/// fixed-depth check only matched when both files sat at the *same* depth,
+/// so e.g. a file in `graph/algorithms/*.rs` calling a method declared in
+/// the shallower `graph/model.rs` was scored as maximally distant (issue #1769).
+fn directory_distance(a: &str, b: &str) -> usize {
+    let chain_a = ancestor_chain(a);
+    let chain_b = ancestor_chain(b);
+    for (i, dir_a) in chain_a.iter().enumerate() {
+        if let Some(j) = chain_b.iter().position(|dir_b| dir_b == dir_a) {
+            return i + j;
+        }
+    }
+    usize::MAX
+}
+
 /// Compute proximity-based confidence for call resolution.
-/// Mirrors `computeConfidence()` in builder.js.
+/// Mirrors `computeConfidence()` in resolve.ts.
 pub fn compute_confidence(
     caller_file: &str,
     target_file: &str,
@@ -275,24 +309,12 @@ pub fn compute_confidence(
         .map(|p| p.display().to_string())
         .unwrap_or_default();
 
-    if caller_dir == target_dir {
-        return 0.7;
-    }
-
-    let caller_parent = Path::new(&caller_dir)
-        .parent()
-        .map(|p| p.display().to_string())
-        .unwrap_or_default();
-    let target_parent = Path::new(&target_dir)
-        .parent()
-        .map(|p| p.display().to_string())
-        .unwrap_or_default();
-
-    if caller_parent == target_parent {
-        return 0.5;
+    match directory_distance(&caller_dir, &target_dir) {
+        0 => 0.7, // same directory
+        1 => 0.6, // direct parent/child directory
+        2 => 0.5, // sibling directories, or a grandparent/grandchild pair
+        _ => 0.3,
     }
-
-    0.3
 }
 
 /// Batch resolve multiple imports (parallelized with rayon).
@@ -430,4 +452,84 @@ mod tests {
         );
         assert_eq!(result, "src/utils.ts");
     }
+
+    // Regression tests for #1769: a fixed-depth "grandparent equality" check
+    // used to compare the parent of `caller_dir` to the parent of `target_dir`,
+    // which only matched when both files sat at the *same* depth. A file in a
+    // subdirectory calling a method declared in its direct parent directory
+    // (e.g. `graph/algorithms/bfs.rs` calling `graph/model.rs`) was scored as
+    // maximally distant (0.3) purely because the two files were nested at
+    // different depths — well below the 0.5 threshold used by the call-edge
+    // resolver's typed-method lookup, silently dropping the call edge.
+
+    #[test]
+    fn compute_confidence_scores_parent_child_dirs_above_resolver_threshold() {
+        let conf = compute_confidence("src/graph/algorithms/bfs.rs", "src/graph/model.rs", None);
+        assert!(conf >= 0.5, "expected >= 0.5, got {conf}");
+    }
+
+    #[test]
+    fn compute_confidence_is_symmetric_for_parent_child_dirs() {
+        let caller_deeper =
+            compute_confidence("src/graph/algorithms/bfs.rs", "src/graph/model.rs", None);
+        let target_deeper =
+            compute_confidence("src/graph/model.rs", "src/graph/algorithms/bfs.rs", None);
+        assert_eq!(caller_deeper, target_deeper);
+    }
+
+    #[test]
+    fn compute_confidence_ranks_parent_child_between_same_dir_and_sibling() {
+        let same_dir = compute_confidence("src/graph/a.rs", "src/graph/b.rs", None);
+        let parent_child =
+            compute_confidence("src/graph/algorithms/bfs.rs", "src/graph/model.rs", None);
+        // True siblings: both one level below `src`, at equal depth.
+        let sibling = compute_confidence("src/graph/a.rs", "src/features/b.rs", None);
+        assert!(same_dir > parent_child);
+        assert!(parent_child > sibling);
+    }
+
+    #[test]
+    fn compute_confidence_scores_two_level_nesting_at_or_above_sibling_tier() {
+        // the graph/algorithms/leiden/*.rs -> graph/model.rs shape from #1769.
+        let conf = compute_confidence(
+            "src/graph/algorithms/leiden/cpm.rs",
+            "src/graph/model.rs",
+            None,
+        );
+        assert!(conf >= 0.5, "expected >= 0.5, got {conf}");
+    }
+
+    #[test]
+    fn compute_confidence_still_scores_unrelated_deep_files_as_distant() {
+        let conf = compute_confidence(
+            "src/graph/algorithms/leiden/cpm.rs",
+            "src/mcp/server.rs",
+            None,
+        );
+        assert!(conf < 0.5, "expected < 0.5, got {conf}");
+    }
+
+    #[test]
+    fn directory_distance_same_dir_is_zero() {
+        assert_eq!(directory_distance("src/graph", "src/graph"), 0);
+    }
+
+    #[test]
+    fn directory_distance_direct_parent_child_is_one() {
+        assert_eq!(directory_distance("src/graph/algorithms", "src/graph"), 1);
+        assert_eq!(directory_distance("src/graph", "src/graph/algorithms"), 1);
+    }
+
+    #[test]
+    fn directory_distance_siblings_is_two() {
+        // Both dirs are one level below `src` — true siblings at equal depth.
+        assert_eq!(directory_distance("src/graph", "src/features"), 2);
+    }
+
+    #[test]
+    fn directory_distance_unequal_depth_non_siblings_is_three() {
+        // `algorithms` is nested inside `graph`, which is a sibling of `features` —
+        // not a direct sibling pair despite sharing the `src` ancestor.
+        assert_eq!(directory_distance("src/graph/algorithms", "src/features"), 3);
+    }
 }

src/domain/graph/resolve.ts

@@ -461,6 +461,41 @@ function resolveImportPathJS(
   return normalizePath(path.relative(rootDir, resolved));
 }
 
+/** All ancestor directories of `dir`, starting with `dir` itself, walking up to the root. */
+function ancestorChain(dir: string): string[] {
+  const chain = [dir];
+  let cur = dir;
+  for (;;) {
+    const parent = path.dirname(cur);
+    if (parent === cur) return chain; // reached root ('.', '/', or a drive root)
+    chain.push(parent);
+    cur = parent;
+  }
+}
+
+/**
+ * Directory-tree distance between two directories: hops up from `a` to the
+ * nearest ancestor shared with `b`, plus hops down from there to `b`.
+ *
+ * Symmetric and depth-independent — unlike a fixed-depth equality check
+ * (e.g. comparing `dirname(dirname(a))` to `dirname(dirname(b))`, as this
+ * function used to), this correctly scores both sibling directories (common
+ * parent) and direct ancestor/descendant directories (one nested inside the
+ * other) regardless of how deep either path is. The fixed-depth check only
+ * matched when both files sat at the *same* depth, so e.g. a file in
+ * `graph/algorithms/*.ts` calling a method declared in the shallower
+ * `graph/model.ts` was scored as maximally distant (issue #1769).
+ */
+function directoryDistance(a: string, b: string): number {
+  const chainA = ancestorChain(a);
+  const chainB = ancestorChain(b);
+  for (let i = 0; i < chainA.length; i++) {
+    const j = chainB.indexOf(chainA[i]!);
+    if (j !== -1) return i + j;
+  }
+  return Infinity;
+}
+
 function computeConfidenceJS(
   callerFile: string,
   targetFile: string,
@@ -471,10 +506,10 @@ function computeConfidenceJS(
   if (importedFrom === targetFile) return 1.0;
   // Workspace-resolved imports get high confidence even across package boundaries
   if (importedFrom && _workspaceResolvedPaths.has(importedFrom)) return 0.95;
-  if (path.dirname(callerFile) === path.dirname(targetFile)) return 0.7;
-  const callerParent = path.dirname(path.dirname(callerFile));
-  const targetParent = path.dirname(path.dirname(targetFile));
-  if (callerParent === targetParent) return 0.5;
+  const dist = directoryDistance(path.dirname(callerFile), path.dirname(targetFile));
+  if (dist === 0) return 0.7; // same directory
+  if (dist === 1) return 0.6; // direct parent/child directory
+  if (dist === 2) return 0.5; // sibling directories, or a grandparent/grandchild pair
   return 0.3;
 }
 

tests/integration/issue-1769-parent-dir-receiver-typed-call.test.ts

@@ -0,0 +1,128 @@
+/**
+ * Regression test for #1769: a function parameter typed with a class name,
+ * declared in a *different, less-deeply-nested directory*, must still
+ * resolve method calls on that parameter back to the class's declaration.
+ *
+ * Root cause: `computeConfidenceJS` (and its Rust mirror `compute_confidence`)
+ * scored directory proximity using a fixed-depth check — comparing the
+ * parent of the caller's directory to the parent of the target's directory.
+ * That check only matched when both files sat at the *same* depth, so a
+ * subdirectory file (e.g. `graph/algorithms/bfs.ts`) calling a method on a
+ * class declared in its direct parent directory (`graph/model.ts`) was
+ * scored as maximally distant (0.3) — well below the 0.5 threshold used by
+ * the call-edge resolver's typed-method lookup (`resolveViaTypedMethod` in
+ * src/domain/graph/resolver/strategy.ts), so the call edge was silently
+ * dropped even though the parameter's type annotation correctly resolved
+ * `foo: Foo` to `typeMap['foo'] = 'Foo'`.
+ *
+ * Setup mirrors the real-world shape from src/graph/algorithms/bfs.ts calling
+ * src/graph/model.ts:
+ *   - model.ts (parent directory): `export class Foo { bar(x): number {...} }`
+ *   - algorithms/consumer.ts (child directory): a function whose PARAMETER is
+ *     typed `foo: Foo` (via type annotation, not `new Foo()` construction)
+ *     calls `foo.bar(x)`.
+ *
+ * Expected: a `calls` edge from `useFoo` to `Foo.bar`, in both engines.
+ */
+
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import Database from 'better-sqlite3';
+import { afterAll, beforeAll, describe, expect, it } from 'vitest';
+import { buildGraph } from '../../src/domain/graph/builder.js';
+
+const TSCONFIG = JSON.stringify({
+  compilerOptions: {
+    target: 'es2022',
+    module: 'esnext',
+    moduleResolution: 'bundler',
+    strict: true,
+  },
+  include: ['**/*.ts'],
+});
+
+const MODEL_TS = `
+export class Foo {
+  bar(x: number): number {
+    return x + 1;
+  }
+}
+`;
+
+// Nested one directory deeper than model.ts — mirrors graph/algorithms/bfs.ts
+// receiving a `graph: CodeGraph` parameter from graph/model.ts.
+const CONSUMER_TS = `
+import type { Foo } from '../model.js';
+
+export function useFoo(foo: Foo, x: number): number {
+  return foo.bar(x);
+}
+`;
+
+let tmpWasm: string;
+let tmpNative: string;
+
+function writeFixture(dir: string): void {
+  fs.writeFileSync(path.join(dir, 'tsconfig.json'), TSCONFIG);
+  // Both files live under a shared `graph/` directory — NOT at the fixture
+  // root — so their relative-path depths mirror the real src/graph/model.ts
+  // vs src/graph/algorithms/bfs.ts shape. Placing model.ts directly at the
+  // fixture root would make `path.dirname()` hit its "." fixed point at the
+  // same recursion depth for both files, which accidentally masks the #1769
+  // bug (the old fixed-depth check happens to coincide at the filesystem
+  // root regardless of the asymmetry it's supposed to detect).
+  fs.mkdirSync(path.join(dir, 'graph', 'algorithms'), { recursive: true });
+  fs.writeFileSync(path.join(dir, 'graph', 'model.ts'), MODEL_TS);
+  fs.writeFileSync(path.join(dir, 'graph', 'algorithms', 'consumer.ts'), CONSUMER_TS);
+}
+
+beforeAll(async () => {
+  tmpWasm = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-1769-wasm-'));
+  writeFixture(tmpWasm);
+
+  tmpNative = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-1769-native-'));
+  writeFixture(tmpNative);
+
+  await Promise.all([
+    buildGraph(tmpWasm, { incremental: false, skipRegistry: true, engine: 'wasm' }),
+    buildGraph(tmpNative, { incremental: false, skipRegistry: true, engine: 'native' }),
+  ]);
+});
+
+afterAll(() => {
+  fs.rmSync(tmpWasm, { recursive: true, force: true });
+  fs.rmSync(tmpNative, { recursive: true, force: true });
+});
+
+function hasCallEdge(dbPath: string, sourceName: string, targetName: string): boolean {
+  const db = new Database(dbPath, { readonly: true });
+  try {
+    const row = db
+      .prepare(
+        `SELECT 1
+         FROM edges e
+         JOIN nodes n1 ON e.source_id = n1.id
+         JOIN nodes n2 ON e.target_id = n2.id
+         WHERE e.kind = 'calls' AND n1.name = ? AND n2.name = ?`,
+      )
+      .get(sourceName, targetName);
+    return row !== undefined;
+  } finally {
+    db.close();
+  }
+}
+
+describe('parameter-typed receiver call to a parent-directory class (#1769)', () => {
+  it('WASM: resolves foo.bar(x) to Foo.bar across a child->parent directory boundary', () => {
+    expect(hasCallEdge(path.join(tmpWasm, '.codegraph', 'graph.db'), 'useFoo', 'Foo.bar')).toBe(
+      true,
+    );
+  });
+
+  it('Native: resolves foo.bar(x) to Foo.bar across a child->parent directory boundary', () => {
+    expect(hasCallEdge(path.join(tmpNative, '.codegraph', 'graph.db'), 'useFoo', 'Foo.bar')).toBe(
+      true,
+    );
+  });
+});