fix(graph): stable USAGE-edge ownership for directory-module nodes

Since #667 every file in a Java/Go package shares a directory-based module
QN that collides with the pipeline's Folder/Project node. Class-level
references resolved their enclosing scope to that shared node, whose
file_path was clobbered by each file's always-emitted Module def — last
writer wins (sequential upsert) or last-merged worker wins (parallel merge)
— so USAGE-edge sources conflated across same-package files and varied run
to run.

Three coordinated changes:
- cbm_gbuf_upsert_node: a Module def colliding with a Project/Folder node
  no longer updates ANY field (the #667 guard only protected the label).
- merge_update_existing: same guard on the parallel worker-gbuf merge path;
  the ID remap stays outside the guard so worker edges still redirect onto
  the canonical node.
- Source-node finders (pass_usages, pass_parallel, pass_calls) treat a
  lookup landing on a Folder/Project container as a miss and fall back to
  the per-file File node (new cbm_pipeline_node_is_dir_container helper).

Adds tests/repro/repro_issue787.c: exact-source-set, 5-run stability, and
>50-file parallel-path guards (red on the unfixed code in both sequential
and parallel flavors).

Distilled from #828: the author's commits lacked DCO sign-off trailers and
could not be cherry-picked; content applied verbatim plus one clang-format
fix in graph_buffer.c.

Closes #787.

Co-authored-by: Tommy Corbett <spde89@gmail.com>
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>

Author: DeusData

Makefile.cbm

@@ -449,6 +449,7 @@ TEST_REPRO_SRCS = \
     tests/repro/repro_new_cypher_limit_zero.c \
     tests/repro/repro_issue363.c \
     tests/repro/repro_issue581.c \
+    tests/repro/repro_issue787.c \
     tests/repro/repro_invariant_calls.c \
     tests/repro/repro_invariant_graph.c \
     tests/repro/repro_invariant_breadth.c \

src/graph_buffer/graph_buffer.c

@@ -635,25 +635,30 @@ int64_t cbm_gbuf_upsert_node(cbm_gbuf_t *gb, const char *label, const char *name
     /* Check if node already exists */
     cbm_gbuf_node_t *existing = cbm_ht_get(gb->node_by_qn, qualified_name);
     if (existing) {
-        /* Update in-place. name/properties are strdup'd BEFORE freeing old ones
-         * (callers may pass existing->name as an argument). label/file_path are
-         * interned: gb_intern returns a stable pool pointer (idempotent even when
-         * label == existing->label), so the old value is replaced, never freed. */
-        char *new_name = heap_strdup(name);
-        char *new_props = properties_json ? heap_strdup(properties_json) : NULL;
-        /* Don't let a per-file "Module" def downgrade a structural directory node
+        /* Don't let a per-file "Module" def touch a structural directory node
          * ("Project" root or "Folder"). In a directory-based-module language
          * (Go/Java) a file's module_qn equals its directory QN: a root file →
          * the project name (== the "Project" node's QN); a file in pkg/ →
          * proj.pkg (== the "pkg/" Folder node's QN). Its always-emitted Module
          * def collides here; the directory node is the package/module container
-         * and must keep its structural label. (Both the sequential upsert and the
-         * parallel local-gbuf merge route through this function.) */
-        if (!(existing->label && label && strcmp(label, "Module") == 0 &&
-              (strcmp(existing->label, "Project") == 0 ||
-               strcmp(existing->label, "Folder") == 0))) {
-            existing->label = (char *)gb_intern(gb, label);
+         * and must keep its structural label AND its own name/file_path/range.
+         * Updating those in place set the shared node's file_path to whichever
+         * same-package file happened to be processed LAST (worker-order
+         * dependent) — the nondeterministic file attribution behind #787 — and
+         * left the Folder node exposed to delete-nodes-by-file on incremental
+         * reindex of that file. Skip the update entirely. (Both the sequential
+         * upsert and the parallel local-gbuf merge route through this function.) */
+        if (existing->label && label && strcmp(label, "Module") == 0 &&
+            (strcmp(existing->label, "Project") == 0 || strcmp(existing->label, "Folder") == 0)) {
+            return existing->id;
         }
+        /* Update in-place. name/properties are strdup'd BEFORE freeing old ones
+         * (callers may pass existing->name as an argument). label/file_path are
+         * interned: gb_intern returns a stable pool pointer (idempotent even when
+         * label == existing->label), so the old value is replaced, never freed. */
+        char *new_name = heap_strdup(name);
+        char *new_props = properties_json ? heap_strdup(properties_json) : NULL;
+        existing->label = (char *)gb_intern(gb, label);
         free(existing->name);
         existing->name = new_name;
         existing->file_path = (char *)gb_intern(gb, file_path);
@@ -1112,15 +1117,30 @@ static void free_remap_entry(const char *key, void *val, void *ud) {
  * label/file_path are re-interned into dst's pool (sn's pointers belong to src). */
 static void merge_update_existing(cbm_gbuf_t *dst, cbm_gbuf_node_t *existing,
                                   const cbm_gbuf_node_t *sn, CBMHashTable **remap) {
-    existing->label = (char *)gb_intern(dst, sn->label);
-    free(existing->name);
-    existing->name = heap_strdup(sn->name);
-    existing->file_path = (char *)gb_intern(dst, sn->file_path);
-    existing->start_line = sn->start_line;
-    existing->end_line = sn->end_line;
-    if (sn->properties_json) {
-        free(existing->properties_json);
-        existing->properties_json = heap_strdup(sn->properties_json);
+    /* Same guard as cbm_gbuf_upsert_node: a per-file "Module" def coming from a
+     * worker-local gbuf must not touch the structural directory node ("Project"
+     * root or "Folder") that shares its QN in a directory-based-module language
+     * (Java/Go). pass_structure seeds Folder/Project nodes on the MAIN gbuf
+     * before the parallel extract, so every worker's always-emitted Module def
+     * for that package collides here; unconditional "src wins" relabelled the
+     * directory node to Module and set its file_path to whichever worker merged
+     * LAST — the nondeterministic USAGE-source misattribution of #787. Keep the
+     * structural node intact; the ID remap below still redirects the worker's
+     * edges onto the canonical node. */
+    bool module_on_container =
+        existing->label && sn->label && strcmp(sn->label, "Module") == 0 &&
+        (strcmp(existing->label, "Project") == 0 || strcmp(existing->label, "Folder") == 0);
+    if (!module_on_container) {
+        existing->label = (char *)gb_intern(dst, sn->label);
+        free(existing->name);
+        existing->name = heap_strdup(sn->name);
+        existing->file_path = (char *)gb_intern(dst, sn->file_path);
+        existing->start_line = sn->start_line;
+        existing->end_line = sn->end_line;
+        if (sn->properties_json) {
+            free(existing->properties_json);
+            existing->properties_json = heap_strdup(sn->properties_json);
+        }
     }
 
     if (sn->id != existing->id) {

src/pipeline/pass_calls.c

@@ -409,6 +409,12 @@ static const cbm_gbuf_node_t *calls_find_source(cbm_pipeline_ctx_t *ctx, const c
     const cbm_gbuf_node_t *src = NULL;
     if (enclosing_qn) {
         src = cbm_gbuf_find_by_qn(ctx->gbuf, enclosing_qn);
+        /* A class-level call in a directory-module language carries the
+         * DIRECTORY module QN, which hits the shared Folder/Project node —
+         * attribute to this file's File node instead (#787). */
+        if (cbm_pipeline_node_is_dir_container(src)) {
+            src = NULL;
+        }
     }
     if (!src) {
         char *fqn = cbm_pipeline_fqn_compute(ctx->project_name, rel, "__file__");

src/pipeline/pass_parallel.c

@@ -1828,6 +1828,12 @@ static const cbm_gbuf_node_t *find_source_node(const cbm_gbuf_t *gbuf, const cha
     const cbm_gbuf_node_t *src = NULL;
     if (enclosing_qn) {
         src = cbm_gbuf_find_by_qn(gbuf, enclosing_qn);
+        /* A class-level reference in a directory-module language carries the
+         * DIRECTORY module QN, which hits the shared Folder/Project node —
+         * attribute to this file's File node instead (#787). */
+        if (cbm_pipeline_node_is_dir_container(src)) {
+            src = NULL;
+        }
     }
     if (!src) {
         char *file_qn = cbm_pipeline_fqn_compute(project, rel, "__file__");

src/pipeline/pass_usages.c

@@ -197,6 +197,12 @@ static const cbm_gbuf_node_t *find_enclosing_node(cbm_pipeline_ctx_t *ctx, const
     const cbm_gbuf_node_t *node = NULL;
     if (func_qn && func_qn[0]) {
         node = cbm_gbuf_find_by_qn(ctx->gbuf, func_qn);
+        /* A class-level reference in a directory-module language carries the
+         * DIRECTORY module QN, which hits the shared Folder/Project node —
+         * attribute to this file's File node instead (#787). */
+        if (cbm_pipeline_node_is_dir_container(node)) {
+            node = NULL;
+        }
     }
     if (!node) {
         char *file_qn = cbm_pipeline_fqn_compute(ctx->project_name, rel_path, "__file__");

src/pipeline/pipeline_internal.h

@@ -34,6 +34,19 @@
  * out_sz >= strlen(in) + 1 always suffices. Returns out. */
 const char *cbm_route_canon_path(const char *in, char *out, size_t out_sz);
 
+/* True when a graph node is a structural directory container (Folder/Project)
+ * rather than a code node. In a directory-based-module language (Java/Go, see
+ * cbm_lang_module_is_dir) a file's module QN equals its directory QN, so an
+ * enclosing-scope lookup for a CLASS-LEVEL usage/call (enclosing_func_qn ==
+ * module_qn) resolves to the ONE Folder/Project node shared by every file in
+ * that package. Sourcing an edge there conflates all same-package files into a
+ * single source node with an arbitrary file_path (#787). Source-node finders
+ * must treat such a hit as a miss and fall back to the per-file File node. */
+static inline bool cbm_pipeline_node_is_dir_container(const cbm_gbuf_node_t *node) {
+    return node && node->label &&
+           (strcmp(node->label, "Folder") == 0 || strcmp(node->label, "Project") == 0);
+}
+
 /* Time unit conversions */
 #define CBM_NS_PER_SEC 1000000000LL
 #define CBM_US_PER_SEC 1000000LL