ralph-hero-knowledge-index 0.1.26 → 0.1.27

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-knowledge",
-  "version": "0.1.26",
+  "version": "0.1.27",
   "description": "Knowledge graph for ralph-hero: semantic search, relationship traversal, and document indexing across thoughts/ documents. Optional companion to ralph-hero.",
   "author": {
     "name": "Chad Dubiel",

package/.mcp.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "ralph-knowledge": {
       "command": "npx",
-      "args": ["-y", "ralph-hero-knowledge-index@0.1.26"]
+      "args": ["-y", "ralph-hero-knowledge-index@0.1.27"]
     }
   }
 }

package/dist/index.js

@@ -162,7 +162,7 @@ export function createServer(dbPath, opts = {}) {
             const hasTier = memoryTierColumnExists(db);
             const hasChunks = chunksTableExists(db);
             const totalRow = db.db
-                .prepare("SELECT COUNT(*) AS c FROM documents")
+                .prepare("SELECT COUNT(*) AS c FROM documents WHERE is_stub = 0 OR is_stub IS NULL")
                 .get();
             const totalDocuments = totalRow.c;
             const byTier = {
@@ -178,7 +178,9 @@ export function createServer(dbPath, opts = {}) {
             if (hasTier) {
                 const rows = db.db
                     .prepare(`SELECT memory_tier AS tier, COUNT(*) AS c
-               FROM documents GROUP BY memory_tier`)
+               FROM documents
+               WHERE (is_stub = 0 OR is_stub IS NULL)
+               GROUP BY memory_tier`)
                     .all();
                 for (const r of rows) {
                     if (r.tier === "doc" || r.tier === "raw" || r.tier === "reflection") {
@@ -188,7 +190,7 @@ export function createServer(dbPath, opts = {}) {
                 const newRows = db.db
                     .prepare(`SELECT memory_tier AS tier, COUNT(*) AS c
                FROM documents
-               WHERE date IS NOT NULL AND date >= @since
+               WHERE date IS NOT NULL AND date >= @since AND (is_stub = 0 OR is_stub IS NULL)
                GROUP BY memory_tier`)
                     .all({ since });
                 for (const r of newRows) {
@@ -201,7 +203,7 @@ export function createServer(dbPath, opts = {}) {
                 // v2 schema — everything treated as "doc"
                 byTier.doc = totalDocuments;
                 const newDocRow = db.db
-                    .prepare("SELECT COUNT(*) AS c FROM documents WHERE date IS NOT NULL AND date >= ?")
+                    .prepare("SELECT COUNT(*) AS c FROM documents WHERE date IS NOT NULL AND date >= ? AND (is_stub = 0 OR is_stub IS NULL)")
                     .get(since);
                 newSince.doc = newDocRow.c;
             }
@@ -219,7 +221,7 @@ export function createServer(dbPath, opts = {}) {
             if (hasTier) {
                 const row = db.db
                     .prepare(`SELECT date FROM documents
-               WHERE memory_tier = 'reflection' AND date IS NOT NULL
+               WHERE memory_tier = 'reflection' AND date IS NOT NULL AND (is_stub = 0 OR is_stub IS NULL)
                ORDER BY date DESC LIMIT 1`)
                     .get();
                 lastReflectionAt = row?.date ?? null;

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/search.js

@@ -79,6 +79,7 @@ export class FtsSearch {
     search(query, options = {}) {
         const { type, tags, includeSuperseded = false, limit = 20, memoryTier } = options;
         const conditions = ["documents_fts MATCH @query"];
+        conditions.push("(d.is_stub = 0 OR d.is_stub IS NULL)");
         const params = { query: this.escapeFts5Query(query), limit };
         if (!includeSuperseded) {
             conditions.push("d.status IS NOT 'superseded'");

package/dist/search.js.map

@@ -1 +1 @@
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+{"version":3,"file":"search.js","sourceRoot":"","sources":["../src/search.ts"],"names":[],"mappings":"AA8BA,MAAM,OAAO,SAAS;IACH,EAAE,CAAc;IAEjC,YAAY,EAAe;QACzB,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;IACf,CAAC;IAED;;;;OAIG;IACH,cAAc,CAAC,KAAa;QAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC5B,gEAAgE,CACjE,CAAC,GAAG,CAAC,KAAK,CAAgF,CAAC;QAC5F,IAAI,CAAC,GAAG;YAAE,OAAO;QACjB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAChB,oGAAoG,CACrG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;IACrD,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,KAAa;QAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC5B,gEAAgE,CACjE,CAAC,GAAG,CAAC,KAAK,CAAgF,CAAC;QAC5F,IAAI,CAAC,GAAG;YAAE,OAAO;QACjB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAChB,2EAA2E,CAC5E,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;IACrD,CAAC;IAED;;;;OAIG;IACH,WAAW;QACT,4DAA4D;QAC5D,MAAM,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC/B,4EAA4E,CAC7E,CAAC,GAAG,EAAE,CAAC;QACR,IAAI,MAAM;YAAE,OAAO;QACnB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;;;;;;KAQf,CAAC,CAAC;IACL,CAAC;IAED,YAAY;QACV,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;QACtD,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;;;;;;KAQf,CAAC,CAAC;QACH,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;KAGf,CAAC,CAAC;IACL,CAAC;IAEO,eAAe,CAAC,GAAW;QACjC,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAChD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;QACrC,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtE,CAAC;IAED;;;OAGG;IACK,sBAAsB;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE;aACpB,OAAO,CAAC,8BAA8B,CAAC;aACvC,GAAG,EAA6B,CAAC;QACpC,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAAC,CAAC;IACpD,CAAC;IAED,MAAM,CAAC,KAAa,EAAE,UAAyB,EAAE;QAC/C,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,iBAAiB,GAAG,KAAK,EAAE,KAAK,GAAG,EAAE,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;QAElF,MAAM,UAAU,GAAa,CAAC,4BAA4B,CAAC,CAAC;QAC5D,UAAU,CAAC,IAAI,CAAC,sCAAsC,CAAC,CAAC;QACxD,MAAM,MAAM,GAA4B,EAAE,KAAK,EAAE,IAAI,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,CAAC;QAEtF,IAAI,CAAC,iBAAiB,EAAE,CAAC;YACvB,UAAU,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;QAClD,CAAC;QAED,IAAI,IAAI,EAAE,CAAC;YACT,UAAU,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;YAClC,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;QACrB,CAAC;QAED,IAAI,UAAU,IAAI,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,sBAAsB,EAAE,EAAE,CAAC;YACxE,UAAU,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;YAC/C,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;QACjC,CAAC;QAED,IAAI,UAAU,GAAG,EAAE,CAAC;QACpB,IAAI,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,UAAU,GAAG,gCAAgC,CAAC;YAC9C,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YACvD,UAAU,CAAC,IAAI,CAAC,aAAa,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC5D,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE;gBACtB,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC;YAC1B,CAAC,CAAC,CAAC;QACL,CAAC;QAED,MAAM,WAAW,GAAG,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QAE7C,MAAM,GAAG,GAAG;;;;;;;;;;;;QAYR,UAAU;cACJ,WAAW;;;KAGpB,CAAC;QAEF,OAAO,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAmB,CAAC;IAC/D,CAAC;CACF"}

package/dist/traverse.js

@@ -30,6 +30,7 @@ export class Traverser {
         d.date AS docDate
       FROM chain
       LEFT JOIN documents d ON d.id = chain.target_id
+      WHERE d.id IS NULL OR d.is_stub = 0 OR d.is_stub IS NULL
       ORDER BY chain.depth, chain.target_id
     `;
         const params = { fromId, depth };
@@ -74,6 +75,7 @@ export class Traverser {
         d.date AS docDate
       FROM chain
       LEFT JOIN documents d ON d.id = chain.source_id
+      WHERE d.id IS NULL OR d.is_stub = 0 OR d.is_stub IS NULL
       ORDER BY chain.depth, chain.target_id
     `;
         const params = { toId, depth };

package/dist/traverse.js.map

@@ -1 +1 @@
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+{"version":3,"file":"traverse.js","sourceRoot":"","sources":["../src/traverse.ts"],"names":[],"mappings":"AAgBA,MAAM,OAAO,SAAS;IACH,EAAE,CAAc;IAEjC,YAAY,EAAe;QACzB,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;IACf,CAAC;IAED,QAAQ,CAAC,MAAc,EAAE,UAA2B,EAAE;QACpD,MAAM,EAAE,IAAI,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACpC,MAAM,UAAU,GAAG,IAAI,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,CAAC;QAEpD,MAAM,GAAG,GAAG;;;;sCAIsB,UAAU;;;;;;;iCAOf,UAAU;;;;;;;;;;;;;;;KAetC,CAAC;QAEF,MAAM,MAAM,GAA4B,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAC1D,IAAI,IAAI;YAAE,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;QAE7B,MAAM,IAAI,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAS7C,CAAC;QAEH,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACtB,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,GAAG,EAAE,CAAC,CAAC,QAAQ,IAAI,IAAI;gBACrB,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,EAAE;gBAC7D,CAAC,CAAC,IAAI;SACT,CAAC,CAAC,CAAC;IACN,CAAC;IAED,gBAAgB,CAAC,IAAY,EAAE,UAA2B,EAAE;QAC1D,MAAM,EAAE,IAAI,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACpC,MAAM,UAAU,GAAG,IAAI,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,CAAC;QAEpD,MAAM,GAAG,GAAG;;;;oCAIoB,UAAU;;;;;;;iCAOb,UAAU;;;;;;;;;;;;;;;KAetC,CAAC;QAEF,MAAM,MAAM,GAA4B,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC;QACxD,IAAI,IAAI;YAAE,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;QAE7B,MAAM,IAAI,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAS7C,CAAC;QAEH,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACtB,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,GAAG,EAAE,CAAC,CAAC,QAAQ,IAAI,IAAI;gBACrB,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,EAAE;gBAC7D,CAAC,CAAC,IAAI;SACT,CAAC,CAAC,CAAC;IACN,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-hero-knowledge-index",
-  "version": "0.1.26",
+  "version": "0.1.27",
   "type": "module",
   "main": "dist/index.js",
   "bin": {

package/src/__tests__/graph-builder.test.ts

@@ -171,4 +171,32 @@ describe("GraphBuilder", () => {
     expect(edgeToA).toBeDefined();
     expect(graph.source(edgeToA!)).toBe("doc-b");
   });
+
+  describe("stub filtering (GH-897)", () => {
+    it("drops stub-target edges (untyped + typed) and excludes stubs from nodes", () => {
+      const freshDb = new KnowledgeDB(":memory:");
+      freshDb.upsertDocument({
+        id: "real-x",
+        path: "real-x.md",
+        title: "Real X",
+        date: "2026-04-10",
+        type: "research",
+        status: "approved",
+        githubIssue: null,
+        content: "",
+      });
+      freshDb.upsertStubDocument("stub-y");
+      freshDb.addRelationship("real-x", "stub-y", "untyped");
+      freshDb.addRelationship("real-x", "stub-y", "builds_on");
+
+      const g = new GraphBuilder(freshDb).buildGraph();
+      expect(g.hasNode("stub-y")).toBe(false);
+      expect(g.hasNode("real-x")).toBe(true);
+      expect(g.outDegree("real-x")).toBe(0);
+      expect(g.order).toBe(1);
+      expect(g.size).toBe(0);
+
+      freshDb.close();
+    });
+  });
 });

package/src/__tests__/memory-stats.test.ts

@@ -201,4 +201,82 @@ describe("knowledge_memory_stats", () => {
     expect(out.chunks_per_doc_p90).toBe(0);
     expect(out.last_reflection_at).toBeNull();
   });
+
+  describe("stub filtering (GH-897)", () => {
+    it("excludes stubs from total_documents and by_tier on v3 schema", async () => {
+      const mod = await import("../index.js");
+      const { server, db } = mod.createServer(":memory:");
+      ensureV3Schema(db);
+
+      // Two real docs across two tiers.
+      seedDoc(db, "real-doc", "doc", "2026-04-10");
+      seedDoc(db, "real-reflection", "reflection", "2026-04-11");
+
+      // Three stubs (default memory_tier = 'doc' per migration).
+      db.upsertStubDocument("stub-1");
+      db.upsertStubDocument("stub-2");
+      db.upsertStubDocument("stub-3");
+
+      const out = await callStats(server, { since: "1970-01-01T00:00:00Z" });
+      expect(out.total_documents).toBe(2);
+      expect(out.by_tier).toEqual({ doc: 1, raw: 0, reflection: 1 });
+      // new_since unaffected — stubs have date = NULL and never count regardless.
+      expect(out.new_since).toEqual({ doc: 1, raw: 0, reflection: 1 });
+    });
+
+    it("excludes stubs from total on a v2 schema (column absent)", async () => {
+      const mod = await import("../index.js");
+      const { server, db } = mod.createServer(":memory:");
+      // Do NOT call ensureV3Schema; v2 path uses the standalone total query and
+      // assigns it to byTier.doc.
+
+      db.upsertDocument({
+        id: "legacy-real",
+        path: "l.md",
+        title: "Legacy",
+        date: "2026-04-01",
+        type: null,
+        status: null,
+        githubIssue: null,
+        content: "",
+      });
+      db.upsertStubDocument("legacy-stub");
+
+      const out = await callStats(server, { since: "1970-01-01T00:00:00Z" });
+      expect(out.total_documents).toBe(1);
+      expect(out.by_tier).toEqual({ doc: 1, raw: 0, reflection: 0 });
+    });
+
+    it("typed-relationship stubs are filtered identically to untyped wikilink stubs", async () => {
+      const mod = await import("../index.js");
+      const { server, db } = mod.createServer(":memory:");
+      ensureV3Schema(db);
+
+      seedDoc(db, "real-source", "doc", "2026-04-10");
+      // Stub created via typed relationship target.
+      db.upsertStubDocument("typed-stub-target");
+      db.addRelationship("real-source", "typed-stub-target", "builds_on");
+
+      const out = await callStats(server, { since: "1970-01-01T00:00:00Z" });
+      expect(out.total_documents).toBe(1);
+      expect(out.by_tier).toEqual({ doc: 1, raw: 0, reflection: 0 });
+    });
+
+    it("last_reflection_at ignores stubs even if a stub somehow had a date and reflection tier", async () => {
+      const mod = await import("../index.js");
+      const { server, db } = mod.createServer(":memory:");
+      ensureV3Schema(db);
+
+      seedDoc(db, "real-reflection-old", "reflection", "2026-03-01");
+      // Force a stub into the reflection tier with a future date — defense-in-depth check.
+      db.upsertStubDocument("future-reflection-stub");
+      db.db
+        .prepare("UPDATE documents SET memory_tier = 'reflection', date = '2099-01-01' WHERE id = ?")
+        .run("future-reflection-stub");
+
+      const out = await callStats(server, { since: "1970-01-01T00:00:00Z" });
+      // Without the filter, the stub's "2099-01-01" would surface as last_reflection_at.
+      expect(out.last_reflection_at).toBe("2026-03-01");
+    });
+  });
 });

package/src/__tests__/search.test.ts

@@ -242,6 +242,69 @@ describe("FtsSearch", () => {
     });
   });
 
+  describe("stub filtering (GH-897)", () => {
+    it("excludes stub documents from FTS results even when their title matches", () => {
+      // Insert a real doc with a unique marker; stub created via upsertStubDocument.
+      const freshDb = new KnowledgeDB(":memory:");
+      freshDb.upsertDocument({
+        id: "real-doc-marker",
+        path: "thoughts/shared/research/marker.md",
+        title: "Marker Doc",
+        date: "2026-04-25",
+        type: "research",
+        status: "draft",
+        githubIssue: null,
+        content: "unique-marker payload contents",
+      });
+      // Stub whose title matches the marker — would surface without the filter.
+      freshDb.upsertStubDocument("unique-marker-stub-id");
+
+      const freshFts = new FtsSearch(freshDb);
+      // Rebuild AFTER both rows exist so the stub does land in documents_fts —
+      // simulates an install that bumped schema version with stubs already present.
+      freshFts.rebuildIndex();
+
+      const hits = freshFts.search("unique-marker");
+      const ids = hits.map((r) => r.id);
+      expect(ids).toContain("real-doc-marker");
+      expect(ids).not.toContain("unique-marker-stub-id");
+
+      // Even querying the stub id directly returns zero rows.
+      const stubByTitle = freshFts.search("unique-marker-stub-id");
+      const stubIds = stubByTitle.map((r) => r.id);
+      expect(stubIds).not.toContain("unique-marker-stub-id");
+
+      freshDb.close();
+    });
+
+    it("typed-relationship stubs (builds_on target) are filtered identically", () => {
+      const freshDb = new KnowledgeDB(":memory:");
+      freshDb.upsertDocument({
+        id: "real-source",
+        path: "thoughts/shared/plans/source.md",
+        title: "Source Plan",
+        date: "2026-04-25",
+        type: "plan",
+        status: "draft",
+        githubIssue: null,
+        content: "phantom-typed-marker payload",
+      });
+      // Stub created via typed relationship target (builds_on).
+      freshDb.upsertStubDocument("phantom-typed-marker");
+      freshDb.addRelationship("real-source", "phantom-typed-marker", "builds_on");
+
+      const freshFts = new FtsSearch(freshDb);
+      freshFts.rebuildIndex();
+
+      const hits = freshFts.search("phantom-typed-marker");
+      const ids = hits.map((r) => r.id);
+      expect(ids).toContain("real-source"); // matches in content
+      expect(ids).not.toContain("phantom-typed-marker"); // stub excluded
+
+      freshDb.close();
+    });
+  });
+
   describe("ensureTable", () => {
     it("creates FTS table if it does not exist", () => {
       // Create a fresh DB without FTS table

package/src/__tests__/traverse.test.ts

@@ -183,11 +183,137 @@ describe("Traverser — untyped edges", () => {
     expect(types).toContain("builds_on");
   });
 
-  it("stub documents appear as doc in traverse results with title matching stub ID", () => {
+  it("stub documents are filtered out of traverse results (regression for GH-897)", () => {
     const results = traverser.traverse("doc-source", { type: "untyped", depth: 1 });
     const toStub = results.find(r => r.targetId === "unresolved-target");
-    expect(toStub).toBeTruthy();
-    expect(toStub!.doc).not.toBeNull();
-    expect(toStub!.doc!.title).toBe("unresolved-target");
+    expect(toStub).toBeUndefined();
+    // Real-document edges still surface
+    const toReal = results.find(r => r.targetId === "doc-target");
+    expect(toReal).toBeTruthy();
+  });
+});
+
+describe("Traverser — stub filtering (GH-897)", () => {
+  let db: KnowledgeDB;
+  let traverser: Traverser;
+
+  beforeEach(() => {
+    db = new KnowledgeDB(":memory:");
+
+    db.upsertDocument({
+      id: "real-a",
+      path: "thoughts/shared/research/real-a.md",
+      title: "Real A",
+      date: "2026-04-01",
+      type: "research",
+      status: "approved",
+      githubIssue: null,
+      content: "Real document A.",
+    });
+
+    db.upsertDocument({
+      id: "real-b",
+      path: "thoughts/shared/research/real-b.md",
+      title: "Real B",
+      date: "2026-04-02",
+      type: "research",
+      status: "approved",
+      githubIssue: null,
+      content: "Real document B.",
+    });
+
+    // Stubs created via both untyped wikilink and typed relationship paths.
+    db.upsertStubDocument("stub-untyped-target");
+    db.upsertStubDocument("stub-typed-target");
+
+    db.addRelationship("real-a", "stub-untyped-target", "untyped", "context");
+    db.addRelationship("real-a", "stub-typed-target", "builds_on");
+
+    // Stub appears as source_id of an edge to a real doc — exercises incoming filter.
+    db.addRelationship("stub-untyped-target", "real-b", "untyped");
+
+    traverser = new Traverser(db);
+  });
+
+  it("traverse() drops outgoing hops to stub targets (untyped + typed)", () => {
+    const results = traverser.traverse("real-a", { depth: 1 });
+    expect(results).toHaveLength(0);
+    // Sanity: neither stub id appears
+    const targetIds = results.map((r) => r.targetId);
+    expect(targetIds).not.toContain("stub-untyped-target");
+    expect(targetIds).not.toContain("stub-typed-target");
+  });
+
+  it("traverse() with type filter still drops stub targets", () => {
+    const buildsOn = traverser.traverse("real-a", { type: "builds_on", depth: 1 });
+    expect(buildsOn).toHaveLength(0);
+    const untyped = traverser.traverse("real-a", { type: "untyped", depth: 1 });
+    expect(untyped).toHaveLength(0);
+  });
+
+  it("traverseIncoming() returns no rows when only inbound edge is from a stub", () => {
+    const results = traverser.traverseIncoming("real-b", { depth: 1 });
+    expect(results).toHaveLength(0);
+  });
+
+  it("traverseIncoming() on a stub returns only real-source edges, never stub sources", () => {
+    // Asking "who points to this stub?" surfaces real callers (real-a here). The
+    // join in traverseIncoming is on chain.source_id, so the predicate filters by
+    // source-side stub-ness — real sources are preserved, stub sources dropped.
+    const results = traverser.traverseIncoming("stub-untyped-target", { depth: 1 });
+    expect(results).toHaveLength(1);
+    expect(results[0].sourceId).toBe("real-a");
+    // None of the rows have a stub document as source.
+    for (const r of results) {
+      // doc is hydrated from d.title; stubs would have title === sourceId.
+      if (r.doc) {
+        expect(r.doc.title).not.toBe(r.sourceId);
+      }
+    }
+  });
+
+  it("non-regression: real-only chain still works after the stub filter is applied", () => {
+    // Independent fresh DB to verify the canonical fixture still passes through the
+    // updated WHERE clause unchanged.
+    const fresh = new KnowledgeDB(":memory:");
+    fresh.upsertDocument({
+      id: "doc-a",
+      path: "doc-a.md",
+      title: "Foundation",
+      date: "2026-02-01",
+      type: "research",
+      status: "approved",
+      githubIssue: null,
+      content: "",
+    });
+    fresh.upsertDocument({
+      id: "doc-b",
+      path: "doc-b.md",
+      title: "Plan",
+      date: "2026-02-15",
+      type: "plan",
+      status: "draft",
+      githubIssue: null,
+      content: "",
+    });
+    fresh.upsertDocument({
+      id: "doc-c",
+      path: "doc-c.md",
+      title: "Revised Plan",
+      date: "2026-03-01",
+      type: "plan",
+      status: "draft",
+      githubIssue: null,
+      content: "",
+    });
+    fresh.addRelationship("doc-b", "doc-a", "builds_on");
+    fresh.addRelationship("doc-c", "doc-b", "builds_on");
+
+    const t = new Traverser(fresh);
+    const chain = t.traverse("doc-c", { type: "builds_on" });
+    expect(chain).toHaveLength(2);
+    expect(chain[0]).toMatchObject({ sourceId: "doc-c", targetId: "doc-b", depth: 1 });
+    expect(chain[1]).toMatchObject({ sourceId: "doc-b", targetId: "doc-a", depth: 2 });
+    fresh.close();
   });
 });

package/src/index.ts

@@ -193,7 +193,7 @@ export function createServer(dbPath: string, opts: CreateServerOptions = {}) {
         const hasChunks = chunksTableExists(db);
 
         const totalRow = db.db
-          .prepare("SELECT COUNT(*) AS c FROM documents")
+          .prepare("SELECT COUNT(*) AS c FROM documents WHERE is_stub = 0 OR is_stub IS NULL")
           .get() as { c: number };
         const totalDocuments = totalRow.c;
 
@@ -212,7 +212,9 @@ export function createServer(dbPath: string, opts: CreateServerOptions = {}) {
           const rows = db.db
             .prepare(
               `SELECT memory_tier AS tier, COUNT(*) AS c
-               FROM documents GROUP BY memory_tier`,
+               FROM documents
+               WHERE (is_stub = 0 OR is_stub IS NULL)
+               GROUP BY memory_tier`,
             )
             .all() as Array<{ tier: string; c: number }>;
           for (const r of rows) {
@@ -224,7 +226,7 @@ export function createServer(dbPath: string, opts: CreateServerOptions = {}) {
             .prepare(
               `SELECT memory_tier AS tier, COUNT(*) AS c
                FROM documents
-               WHERE date IS NOT NULL AND date >= @since
+               WHERE date IS NOT NULL AND date >= @since AND (is_stub = 0 OR is_stub IS NULL)
                GROUP BY memory_tier`,
             )
             .all({ since }) as Array<{ tier: string; c: number }>;
@@ -238,7 +240,7 @@ export function createServer(dbPath: string, opts: CreateServerOptions = {}) {
           byTier.doc = totalDocuments;
           const newDocRow = db.db
             .prepare(
-              "SELECT COUNT(*) AS c FROM documents WHERE date IS NOT NULL AND date >= ?",
+              "SELECT COUNT(*) AS c FROM documents WHERE date IS NOT NULL AND date >= ? AND (is_stub = 0 OR is_stub IS NULL)",
             )
             .get(since) as { c: number };
           newSince.doc = newDocRow.c;
@@ -262,7 +264,7 @@ export function createServer(dbPath: string, opts: CreateServerOptions = {}) {
           const row = db.db
             .prepare(
               `SELECT date FROM documents
-               WHERE memory_tier = 'reflection' AND date IS NOT NULL
+               WHERE memory_tier = 'reflection' AND date IS NOT NULL AND (is_stub = 0 OR is_stub IS NULL)
                ORDER BY date DESC LIMIT 1`,
             )
             .get() as { date: string } | undefined;

package/src/search.ts

@@ -124,6 +124,7 @@ export class FtsSearch {
     const { type, tags, includeSuperseded = false, limit = 20, memoryTier } = options;
 
     const conditions: string[] = ["documents_fts MATCH @query"];
+    conditions.push("(d.is_stub = 0 OR d.is_stub IS NULL)");
     const params: Record<string, unknown> = { query: this.escapeFts5Query(query), limit };
 
     if (!includeSuperseded) {

package/src/traverse.ts

@@ -49,6 +49,7 @@ export class Traverser {
         d.date AS docDate
       FROM chain
       LEFT JOIN documents d ON d.id = chain.target_id
+      WHERE d.id IS NULL OR d.is_stub = 0 OR d.is_stub IS NULL
       ORDER BY chain.depth, chain.target_id
     `;
 
@@ -106,6 +107,7 @@ export class Traverser {
         d.date AS docDate
       FROM chain
       LEFT JOIN documents d ON d.id = chain.source_id
+      WHERE d.id IS NULL OR d.is_stub = 0 OR d.is_stub IS NULL
       ORDER BY chain.depth, chain.target_id
     `;