fix: reconnect reverse-dep edges correctly when a sibling group's size also changes

reconnectReverseDepEdges (build-edges.ts) and its native mirror
reconnect_reverse_dep_edges (detect_changes.rs) re-attach a reverse-dep
caller's edge to its purged-and-reinserted target using a saved ordinal
rank among same-(name, kind) siblings, falling back to nearest-line
matching whenever the sibling count itself changed since save (a same-named
sibling added or removed in the same edit). That fallback is exactly the
nearest-line heuristic #1752 already proved unreliable once a same-named
group shifts far enough, so the compound scenario (shift + count change in
one incremental build) still produced call edges that diverged from a full
rebuild.

Replaces the ordinal/nearest-line two-tier heuristic with a single
alignment: match old-to-new siblings by rank when the sibling count is
unchanged (subsumes #1752's fix exactly), or by the single dominant
line-shift that best explains the surviving (untouched) siblings when the
count changed. Untouched siblings' own source text is never edited, so they
all shift by the exact same delta regardless of how far the group has
moved — finding that shift correctly identifies which old sibling was
removed (or which new one was added) without guessing based on raw line
proximity, which a uniform shift can fool (confirmed against this repo's
own real #1752 fixture numbers, where a naive minimum-distance alignment
picks the wrong element to drop).

Adds `build.reverseDepAlignmentMaxGroupSize` (default 200) bounding the
alignment's shift-histogram cost for pathologically large sibling groups,
mirrored in both engines' DEFAULTS.

Author: carlos-alm

crates/codegraph-core/src/domain/graph/builder/pipeline.rs

@@ -175,32 +175,50 @@ fn early_exit_result(
     }
 }
 
+/// `(saved_reverse_dep_edges, saved_sibling_groups, removal_reverse_deps,
+/// removed_file_neighbors)` — see `save_and_purge_changed`.
+type SaveAndPurgeResult = (
+    Vec<detect_changes::SavedReverseDepEdge>,
+    HashMap<detect_changes::SiblingGroupKey, Vec<i64>>,
+    Vec<String>,
+    Vec<String>,
+);
+
 /// Save reverse-dep edges (and reverse-deps of removed files) before purging
 /// changed files. Mirrors the JS save-then-purge sequence in `build-edges.ts`
-/// (#1012). Returns `(saved_reverse_dep_edges, removal_reverse_deps,
-/// removed_file_neighbors)` so the pipeline can reconnect edges after Stage 5,
-/// reclassify roles in Stage 8, and (#1839) fold a removed file's
-/// cross-directory neighbors into Stage 8's directory-metrics refresh.
+/// (#1012). Returns `(saved_reverse_dep_edges, saved_sibling_groups,
+/// removal_reverse_deps, removed_file_neighbors)` so the pipeline can
+/// reconnect edges after Stage 5, reclassify roles in Stage 8, and (#1839)
+/// fold a removed file's cross-directory neighbors into Stage 8's
+/// directory-metrics refresh.
 fn save_and_purge_changed(
     conn: &Connection,
     parse_changes: &[&detect_changes::ChangedFile],
     change_result: &detect_changes::ChangeResult,
     opts: &BuildOpts,
     root_dir: &str,
-) -> (Vec<detect_changes::SavedReverseDepEdge>, Vec<String>, Vec<String>) {
+) -> SaveAndPurgeResult {
     let mut saved_reverse_dep_edges: Vec<detect_changes::SavedReverseDepEdge> = Vec::new();
+    let mut saved_sibling_groups: HashMap<detect_changes::SiblingGroupKey, Vec<i64>> =
+        HashMap::new();
     let mut removal_reverse_deps: Vec<String> = Vec::new();
 
     if change_result.is_full_build {
         let has_embeddings = detect_changes::has_embeddings(conn);
         detect_changes::clear_all_graph_data(conn, has_embeddings);
-        return (saved_reverse_dep_edges, removal_reverse_deps, Vec::new());
+        return (
+            saved_reverse_dep_edges,
+            saved_sibling_groups,
+            removal_reverse_deps,
+            Vec::new(),
+        );
     }
 
     let changed_paths: Vec<String> = parse_changes.iter().map(|c| c.rel_path.clone()).collect();
 
     if !opts.no_reverse_deps.unwrap_or(false) {
-        saved_reverse_dep_edges = detect_changes::save_reverse_dep_edges(conn, &changed_paths);
+        (saved_reverse_dep_edges, saved_sibling_groups) =
+            detect_changes::save_reverse_dep_edges(conn, &changed_paths);
 
         if !change_result.removed.is_empty() {
             let removed_set: HashSet<String> = change_result.removed.iter().cloned().collect();
@@ -225,7 +243,12 @@ fn save_and_purge_changed(
         .collect();
     detect_changes::purge_changed_files(conn, &files_to_purge, &[]);
 
-    (saved_reverse_dep_edges, removal_reverse_deps, removed_file_neighbors)
+    (
+        saved_reverse_dep_edges,
+        saved_sibling_groups,
+        removal_reverse_deps,
+        removed_file_neighbors,
+    )
 }
 
 /// Parse a changed-file slice in parallel and key the results by relative path.
@@ -286,11 +309,18 @@ fn resolve_pipeline_imports(
 fn reconnect_saved_reverse_dep_edges(
     conn: &Connection,
     saved: &[detect_changes::SavedReverseDepEdge],
+    saved_sibling_groups: &HashMap<detect_changes::SiblingGroupKey, Vec<i64>>,
+    max_align_group_size: usize,
 ) {
     if saved.is_empty() {
         return;
     }
-    let (reconnected, dropped) = detect_changes::reconnect_reverse_dep_edges(conn, saved);
+    let (reconnected, dropped) = detect_changes::reconnect_reverse_dep_edges(
+        conn,
+        saved,
+        saved_sibling_groups,
+        max_align_group_size,
+    );
     if dropped > 0 {
         eprintln!(
             "[codegraph] reconnect_reverse_dep_edges: {reconnected} reconnected, {dropped} dropped (target nodes not found)"
@@ -528,7 +558,7 @@ pub fn run_pipeline(
     // Stage 3b: save reverse-dep edges (incremental) or clear all (full),
     // then purge changed files. Returns the saved edges for Stage 7
     // reconnect and the removal reverse-dep set for Stage 8 reclassification.
-    let (saved_reverse_dep_edges, removal_reverse_deps, removed_file_neighbors) =
+    let (saved_reverse_dep_edges, saved_sibling_groups, removal_reverse_deps, removed_file_neighbors) =
         save_and_purge_changed(conn, &parse_changes, &change_result, &opts, root_dir);
 
     // ── Stage 4: Parse files ───────────────────────────────────────────
@@ -639,7 +669,12 @@ pub fn run_pipeline(
     )
     .map_err(|e| format!("call edge insertion failed: {e}"))?;
 
-    reconnect_saved_reverse_dep_edges(conn, &saved_reverse_dep_edges);
+    reconnect_saved_reverse_dep_edges(
+        conn,
+        &saved_reverse_dep_edges,
+        &saved_sibling_groups,
+        config.build.reverse_dep_alignment_max_group_size,
+    );
 
     // Now that edges reflect this revision, commit file_hashes for the
     // changed files (#1731). Deferred from Stage 5 — see the comment there.