@danielblomma/cortex-mcp 0.4.5 → 0.6.5

package/scaffold/mcp/src/graph.ts

@@ -1,6 +1,7 @@
 import fs from "node:fs";
 import path from "node:path";
 import ryugraph, { type Connection, type Database, type QueryResult } from "ryugraph";
+import { readJsonl, asString, asNumber, asBoolean } from "./jsonl.js";
 import { DB_PATH, DEFAULT_RANKING, PATHS } from "./paths.js";
 import type {
   AdrRecord,
@@ -8,9 +9,11 @@ import type {
   ContextData,
   DocumentRecord,
   JsonObject,
-  JsonValue,
+  ModuleRecord,
+  ProjectRecord,
   RankingWeights,
   RelationRecord,
+  RelationType,
   RuleRecord,
   UnknownRow
 } from "./types.js";
@@ -31,6 +34,33 @@ let ryuLastInitAttemptAt = 0;
 let ryuGraphSignature: string | null = null;
 
 const RYU_INIT_RETRY_INTERVAL_MS = 2000;
+const REQUIRED_GRAPH_MANIFEST_COUNT_KEYS = [
+  "files",
+  "rules",
+  "adrs",
+  "chunks",
+  "constrains",
+  "implements",
+  "supersedes",
+  "defines",
+  "calls",
+  "imports",
+  "calls_sql",
+  "uses_config_key",
+  "uses_resource_key",
+  "uses_setting_key",
+  "modules",
+  "projects",
+  "contains",
+  "contains_module",
+  "exports",
+  "includes_file",
+  "references_project",
+  "uses_resource",
+  "uses_setting",
+  "uses_config",
+  "transforms_config"
+] as const;
 
 function readFileIfExists(filePath: string): string | null {
   if (!fs.existsSync(filePath)) {
@@ -39,38 +69,6 @@ function readFileIfExists(filePath: string): string | null {
   return fs.readFileSync(filePath, "utf8");
 }
 
-function readJsonl(filePath: string): JsonObject[] {
-  const raw = readFileIfExists(filePath);
-  if (!raw) {
-    return [];
-  }
-
-  return raw
-    .split(/\r?\n/)
-    .map((line) => line.trim())
-    .filter(Boolean)
-    .map((line) => {
-      try {
-        return JSON.parse(line) as JsonObject;
-      } catch {
-        return null;
-      }
-    })
-    .filter((value): value is JsonObject => value !== null);
-}
-
-function asString(value: JsonValue | undefined, fallback = ""): string {
-  return typeof value === "string" ? value : fallback;
-}
-
-function asNumber(value: JsonValue | undefined, fallback = 0): number {
-  return typeof value === "number" && Number.isFinite(value) ? value : fallback;
-}
-
-function asBoolean(value: JsonValue | undefined, fallback = false): boolean {
-  return typeof value === "boolean" ? value : fallback;
-}
-
 function asStringUnknown(value: unknown, fallback = ""): string {
   if (typeof value === "string") return value;
   if (typeof value === "number" || typeof value === "bigint" || typeof value === "boolean") {
@@ -164,9 +162,11 @@ function parseChunkEntities(raw: JsonObject[]): ChunkRecord[] {
         kind: asString(item.kind, "chunk"),
         signature: asString(item.signature),
         body: asString(item.body),
+        description: asString(item.description),
         start_line: asNumber(item.start_line),
         end_line: asNumber(item.end_line),
         language: asString(item.language),
+        exported: asBoolean(item.exported, false),
         updated_at: asString(item.updated_at),
         source_of_truth: asBoolean(item.source_of_truth, false),
         trust_level: asNumber(item.trust_level, 60),
@@ -176,6 +176,56 @@ function parseChunkEntities(raw: JsonObject[]): ChunkRecord[] {
     .filter((item): item is ChunkRecord => item !== null);
 }
 
+function parseModuleEntities(raw: JsonObject[]): ModuleRecord[] {
+  return raw
+    .map((item) => {
+      const id = asString(item.id);
+      if (!id) {
+        return null;
+      }
+
+      return {
+        id,
+        path: asString(item.path),
+        name: asString(item.name),
+        summary: asString(item.summary),
+        file_count: asNumber(item.file_count, 0),
+        exported_symbols: asString(item.exported_symbols),
+        updated_at: asString(item.updated_at),
+        source_of_truth: asBoolean(item.source_of_truth, false),
+        trust_level: asNumber(item.trust_level, 75),
+        status: asString(item.status, "active")
+      };
+    })
+    .filter((item): item is ModuleRecord => item !== null);
+}
+
+function parseProjectEntities(raw: JsonObject[]): ProjectRecord[] {
+  return raw
+    .map((item) => {
+      const id = asString(item.id);
+      if (!id) {
+        return null;
+      }
+
+      return {
+        id,
+        path: asString(item.path),
+        name: asString(item.name),
+        kind: asString(item.kind, "project"),
+        language: asString(item.language, "dotnet"),
+        target_framework: asString(item.target_framework),
+        summary: asString(item.summary),
+        file_count: asNumber(item.file_count, 0),
+        updated_at: asString(item.updated_at),
+        source_of_truth: asBoolean(item.source_of_truth, false),
+        trust_level: asNumber(item.trust_level, 80),
+        status: asString(item.status, "active")
+      };
+    })
+    .filter((item): item is ProjectRecord => item !== null);
+}
+
 function parseRuleEntities(raw: JsonObject[]): RuleRecord[] {
   return raw
     .map((item) => {
@@ -273,7 +323,7 @@ function parseRulesYaml(yamlText: string | null): RuleRecord[] {
 
 function parseRelations(
   raw: JsonObject[],
-  relation: RelationRecord["relation"],
+  relation: RelationType,
   noteFields: string[] = ["note", "reason"]
 ): RelationRecord[] {
   return raw
@@ -379,6 +429,28 @@ function buildMissingDbMessage(): string {
   return `RyuGraph DB not found at ${DB_PATH}. Run ${loadCommand} (or ${bootstrapCommand} on cold start).`;
 }
 
+function buildIncompatibleGraphMessage(missingKeys: string[]): string {
+  const loadCommand = "./scripts/context.sh graph-load";
+  const missing = missingKeys.join(", ");
+  return `RyuGraph manifest is missing schema keys (${missing}). Run ${loadCommand} to rebuild the graph DB.`;
+}
+
+function readGraphManifestMissingKeys(): string[] {
+  if (!fs.existsSync(PATHS.graphManifest)) {
+    return [...REQUIRED_GRAPH_MANIFEST_COUNT_KEYS];
+  }
+
+  try {
+    const raw = JSON.parse(fs.readFileSync(PATHS.graphManifest, "utf8")) as {
+      counts?: Record<string, unknown>;
+    };
+    const counts = raw.counts ?? {};
+    return REQUIRED_GRAPH_MANIFEST_COUNT_KEYS.filter((key) => !(key in counts));
+  } catch {
+    return [...REQUIRED_GRAPH_MANIFEST_COUNT_KEYS];
+  }
+}
+
 async function closeRyuGraphResources(): Promise<void> {
   const currentConnection = ryuConnection;
   const currentDb = ryuDb;
@@ -435,6 +507,12 @@ async function getRyuGraphConnection(forceReload = false): Promise<Connection |
     return null;
   }
 
+  const missingManifestKeys = readGraphManifestMissingKeys();
+  if (missingManifestKeys.length > 0) {
+    await resetRyuGraphState(buildIncompatibleGraphMessage(missingManifestKeys));
+    return null;
+  }
+
   try {
     const nextDb = new ryugraph.Database(DB_PATH, undefined, undefined, true);
     const nextConnection = new ryugraph.Connection(nextDb);
@@ -539,9 +617,11 @@ function parseRyuGraphChunks(rows: UnknownRow[]): ChunkRecord[] {
         kind: asStringUnknown(row.kind, "chunk"),
         signature: asStringUnknown(row.signature),
         body: asStringUnknown(row.body),
+        description: asStringUnknown(row.description),
         start_line: asNumberUnknown(row.start_line),
         end_line: asNumberUnknown(row.end_line),
         language: asStringUnknown(row.language),
+        exported: asBooleanUnknown(row.exported, false),
         updated_at: asStringUnknown(row.updated_at),
         source_of_truth: asBooleanUnknown(row.source_of_truth, false),
         trust_level: asNumberUnknown(row.trust_level, 60),
@@ -551,9 +631,59 @@ function parseRyuGraphChunks(rows: UnknownRow[]): ChunkRecord[] {
     .filter((value): value is ChunkRecord => value !== null);
 }
 
+function parseRyuGraphModules(rows: UnknownRow[]): ModuleRecord[] {
+  return rows
+    .map((row) => {
+      const id = asStringUnknown(row.id);
+      if (!id) {
+        return null;
+      }
+
+      return {
+        id,
+        path: asStringUnknown(row.path),
+        name: asStringUnknown(row.name),
+        summary: asStringUnknown(row.summary),
+        file_count: asNumberUnknown(row.file_count, 0),
+        exported_symbols: asStringUnknown(row.exported_symbols),
+        updated_at: asStringUnknown(row.updated_at),
+        source_of_truth: asBooleanUnknown(row.source_of_truth, false),
+        trust_level: asNumberUnknown(row.trust_level, 75),
+        status: asStringUnknown(row.status, "active")
+      };
+    })
+    .filter((value): value is ModuleRecord => value !== null);
+}
+
+function parseRyuGraphProjects(rows: UnknownRow[]): ProjectRecord[] {
+  return rows
+    .map((row) => {
+      const id = asStringUnknown(row.id);
+      if (!id) {
+        return null;
+      }
+
+      return {
+        id,
+        path: asStringUnknown(row.path),
+        name: asStringUnknown(row.name),
+        kind: asStringUnknown(row.kind, "project"),
+        language: asStringUnknown(row.language, "dotnet"),
+        target_framework: asStringUnknown(row.target_framework),
+        summary: asStringUnknown(row.summary),
+        file_count: asNumberUnknown(row.file_count, 0),
+        updated_at: asStringUnknown(row.updated_at),
+        source_of_truth: asBooleanUnknown(row.source_of_truth, false),
+        trust_level: asNumberUnknown(row.trust_level, 80),
+        status: asStringUnknown(row.status, "active")
+      };
+    })
+    .filter((value): value is ProjectRecord => value !== null);
+}
+
 function parseRyuGraphRelations(
   rows: UnknownRow[],
-  relation: RelationRecord["relation"],
+  relation: RelationType,
   noteField: string
 ): RelationRecord[] {
   return rows
@@ -578,15 +708,37 @@ export async function loadContextData(): Promise<ContextData> {
   const cachedDocuments = parseDocuments(readJsonl(PATHS.documents));
   const cachedAdrs = parseAdrs(readJsonl(PATHS.adrEntities));
   const cachedChunks = parseChunkEntities(readJsonl(PATHS.chunkEntities));
+  const cachedModules = parseModuleEntities(readJsonl(PATHS.moduleEntities));
+  const cachedProjects = parseProjectEntities(readJsonl(PATHS.projectEntities));
   const cachedChunkRelations = [
+    ...parseRelations(readJsonl(PATHS.definesRelations), "DEFINES"),
     ...parseRelations(readJsonl(PATHS.callsRelations), "CALLS", ["call_type"]),
-    ...parseRelations(readJsonl(PATHS.importsRelations), "IMPORTS", ["import_name"])
+    ...parseRelations(readJsonl(PATHS.importsRelations), "IMPORTS", ["import_name"]),
+    ...parseRelations(readJsonl(PATHS.callsSqlRelations), "CALLS_SQL"),
+    ...parseRelations(readJsonl(PATHS.usesConfigKeyRelations), "USES_CONFIG_KEY"),
+    ...parseRelations(readJsonl(PATHS.usesResourceKeyRelations), "USES_RESOURCE_KEY"),
+    ...parseRelations(readJsonl(PATHS.usesSettingKeyRelations), "USES_SETTING_KEY")
+  ];
+  const cachedModuleRelations = [
+    ...parseRelations(readJsonl(PATHS.containsRelations), "CONTAINS"),
+    ...parseRelations(readJsonl(PATHS.containsModuleRelations), "CONTAINS_MODULE"),
+    ...parseRelations(readJsonl(PATHS.exportsRelations), "EXPORTS")
+  ];
+  const cachedProjectRelations = [
+    ...parseRelations(readJsonl(PATHS.includesFileRelations), "INCLUDES_FILE"),
+    ...parseRelations(readJsonl(PATHS.referencesProjectRelations), "REFERENCES_PROJECT"),
+    ...parseRelations(readJsonl(PATHS.usesResourceRelations), "USES_RESOURCE"),
+    ...parseRelations(readJsonl(PATHS.usesSettingRelations), "USES_SETTING"),
+    ...parseRelations(readJsonl(PATHS.usesConfigRelations), "USES_CONFIG"),
+    ...parseRelations(readJsonl(PATHS.transformsConfigRelations), "TRANSFORMS_CONFIG")
   ];
   const cachedRelations = [
     ...parseRelations(readJsonl(PATHS.constrainsRelations), "CONSTRAINS"),
     ...parseRelations(readJsonl(PATHS.implementsRelations), "IMPLEMENTS"),
     ...parseRelations(readJsonl(PATHS.supersedesRelations), "SUPERSEDES"),
-    ...cachedChunkRelations
+    ...cachedChunkRelations,
+    ...cachedModuleRelations,
+    ...cachedProjectRelations
   ];
 
   const yamlRules = parseRulesYaml(readFileIfExists(PATHS.rulesYaml));
@@ -600,6 +752,8 @@ export async function loadContextData(): Promise<ContextData> {
       adrs: cachedAdrs,
       rules: cachedRules,
       chunks: cachedChunks,
+      modules: cachedModules,
+      projects: cachedProjects,
       relations: cachedRelations,
       ranking,
       source: "cache",
@@ -608,97 +762,42 @@ export async function loadContextData(): Promise<ContextData> {
   }
 
   try {
-    const [fileRows, ruleRows, adrRows, chunkRows, constrainsRows, implementsRows, supersedesRows] =
-      await Promise.all([
-        queryRows(
-          connection,
-          `
-          MATCH (f:File)
-          RETURN
-            f.id AS id,
-            f.path AS path,
-            f.kind AS kind,
-            f.excerpt AS excerpt,
-            f.updated_at AS updated_at,
-            f.source_of_truth AS source_of_truth,
-            f.trust_level AS trust_level,
-            f.status AS status;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (r:Rule)
-          RETURN
-            r.id AS id,
-            r.title AS title,
-            r.body AS body,
-            r.scope AS scope,
-            r.priority AS priority,
-            r.updated_at AS updated_at,
-            r.source_of_truth AS source_of_truth,
-            r.trust_level AS trust_level,
-            r.status AS status;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (a:ADR)
-          RETURN
-            a.id AS id,
-            a.path AS path,
-            a.title AS title,
-            a.body AS body,
-            a.decision_date AS decision_date,
-            a.supersedes_id AS supersedes_id,
-            a.source_of_truth AS source_of_truth,
-            a.trust_level AS trust_level,
-            a.status AS status;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (c:Chunk)
-          RETURN
-            c.id AS id,
-            c.file_id AS file_id,
-            c.name AS name,
-            c.kind AS kind,
-            c.signature AS signature,
-            c.body AS body,
-            c.start_line AS start_line,
-            c.end_line AS end_line,
-            c.language AS language,
-            c.updated_at AS updated_at,
-            c.source_of_truth AS source_of_truth,
-            c.trust_level AS trust_level,
-            c.status AS status;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (r:Rule)-[c:CONSTRAINS]->(f:File)
-          RETURN r.id AS from, f.id AS to, c.note AS note;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (f:File)-[i:IMPLEMENTS]->(r:Rule)
-          RETURN f.id AS from, r.id AS to, i.note AS note;
-        `
-        ),
-        queryRows(
-          connection,
-          `
-          MATCH (a1:ADR)-[s:SUPERSEDES]->(a2:ADR)
-          RETURN a1.id AS from, a2.id AS to, s.reason AS note;
-        `
-        )
-      ]);
+    const ryuQueries = await Promise.all([
+      queryRows(connection, `MATCH (f:File) RETURN f.id AS id, f.path AS path, f.kind AS kind, f.excerpt AS excerpt, f.updated_at AS updated_at, f.source_of_truth AS source_of_truth, f.trust_level AS trust_level, f.status AS status;`),
+      queryRows(connection, `MATCH (r:Rule) RETURN r.id AS id, r.title AS title, r.body AS body, r.scope AS scope, r.priority AS priority, r.updated_at AS updated_at, r.source_of_truth AS source_of_truth, r.trust_level AS trust_level, r.status AS status;`),
+      queryRows(connection, `MATCH (a:ADR) RETURN a.id AS id, a.path AS path, a.title AS title, a.body AS body, a.decision_date AS decision_date, a.supersedes_id AS supersedes_id, a.source_of_truth AS source_of_truth, a.trust_level AS trust_level, a.status AS status;`),
+      queryRows(connection, `MATCH (c:Chunk) RETURN c.id AS id, c.file_id AS file_id, c.name AS name, c.kind AS kind, c.signature AS signature, c.body AS body, c.description AS description, c.start_line AS start_line, c.end_line AS end_line, c.language AS language, c.exported AS exported, c.updated_at AS updated_at, c.source_of_truth AS source_of_truth, c.trust_level AS trust_level, c.status AS status;`),
+      queryRows(connection, `MATCH (m:Module) RETURN m.id AS id, m.path AS path, m.name AS name, m.summary AS summary, m.file_count AS file_count, m.exported_symbols AS exported_symbols, m.updated_at AS updated_at, m.source_of_truth AS source_of_truth, m.trust_level AS trust_level, m.status AS status;`),
+      queryRows(connection, `MATCH (p:Project) RETURN p.id AS id, p.path AS path, p.name AS name, p.kind AS kind, p.language AS language, p.target_framework AS target_framework, p.summary AS summary, p.file_count AS file_count, p.updated_at AS updated_at, p.source_of_truth AS source_of_truth, p.trust_level AS trust_level, p.status AS status;`),
+      queryRows(connection, `MATCH (r:Rule)-[c:CONSTRAINS]->(f:File) RETURN r.id AS from, f.id AS to, c.note AS note;`),
+      queryRows(connection, `MATCH (f:File)-[i:IMPLEMENTS]->(r:Rule) RETURN f.id AS from, r.id AS to, i.note AS note;`),
+      queryRows(connection, `MATCH (a1:ADR)-[s:SUPERSEDES]->(a2:ADR) RETURN a1.id AS from, a2.id AS to, s.reason AS note;`),
+      queryRows(connection, `MATCH (f:File)-[:DEFINES]->(c:Chunk) RETURN f.id AS from, c.id AS to;`),
+      queryRows(connection, `MATCH (c1:Chunk)-[ca:CALLS]->(c2:Chunk) RETURN c1.id AS from, c2.id AS to, ca.call_type AS call_type;`),
+      queryRows(connection, `MATCH (c:Chunk)-[im:IMPORTS]->(f:File) RETURN c.id AS from, f.id AS to, im.import_name AS import_name;`),
+      queryRows(connection, `MATCH (f:File)-[cs:CALLS_SQL]->(c:Chunk) RETURN f.id AS from, c.id AS to, cs.note AS note;`),
+      queryRows(connection, `MATCH (f:File)-[uck:USES_CONFIG_KEY]->(c:Chunk) RETURN f.id AS from, c.id AS to, uck.note AS note;`),
+      queryRows(connection, `MATCH (f:File)-[urk:USES_RESOURCE_KEY]->(c:Chunk) RETURN f.id AS from, c.id AS to, urk.note AS note;`),
+      queryRows(connection, `MATCH (f:File)-[usk:USES_SETTING_KEY]->(c:Chunk) RETURN f.id AS from, c.id AS to, usk.note AS note;`),
+      queryRows(connection, `MATCH (m:Module)-[:CONTAINS]->(f:File) RETURN m.id AS from, f.id AS to;`),
+      queryRows(connection, `MATCH (m1:Module)-[:CONTAINS_MODULE]->(m2:Module) RETURN m1.id AS from, m2.id AS to;`),
+      queryRows(connection, `MATCH (m:Module)-[:EXPORTS]->(c:Chunk) RETURN m.id AS from, c.id AS to;`),
+      queryRows(connection, `MATCH (p:Project)-[:INCLUDES_FILE]->(f:File) RETURN p.id AS from, f.id AS to;`),
+      queryRows(connection, `MATCH (p1:Project)-[rp:REFERENCES_PROJECT]->(p2:Project) RETURN p1.id AS from, p2.id AS to, rp.note AS note;`),
+      queryRows(connection, `MATCH (f1:File)-[ur:USES_RESOURCE]->(f2:File) RETURN f1.id AS from, f2.id AS to, ur.note AS note;`),
+      queryRows(connection, `MATCH (f1:File)-[us:USES_SETTING]->(f2:File) RETURN f1.id AS from, f2.id AS to, us.note AS note;`),
+      queryRows(connection, `MATCH (f1:File)-[uc:USES_CONFIG]->(f2:File) RETURN f1.id AS from, f2.id AS to, uc.note AS note;`),
+      queryRows(connection, `MATCH (f1:File)-[tc:TRANSFORMS_CONFIG]->(f2:File) RETURN f1.id AS from, f2.id AS to, tc.note AS note;`)
+    ]);
+
+    // Named destructuring to avoid positional misalignment with 14 parallel queries
+    const [
+      fileRows, ruleRows, adrRows, chunkRows, moduleRows, projectRows, // entities
+      constrainsRows, implementsRows, supersedesRows,               // core relations
+      definesRows, callsRows, importsRows, callsSqlRows, usesConfigKeyRows, usesResourceKeyRows, usesSettingKeyRows, // chunk relations
+      containsRows, containsModuleRows, exportsRows,                // module relations
+      includesFileRows, referencesProjectRows, usesResourceRows, usesSettingRows, usesConfigRows, transformsConfigRows // project/file relations
+    ] = ryuQueries;
 
     const contentById = new Map(cachedDocuments.map((doc) => [doc.id, doc.content]));
 
@@ -706,10 +805,28 @@ export async function loadContextData(): Promise<ContextData> {
     const ryuRules = parseRyuGraphRules(ruleRows);
     const ryuAdrs = parseRyuGraphAdrs(adrRows);
     const ryuChunks = parseRyuGraphChunks(chunkRows);
+    const ryuModules = parseRyuGraphModules(moduleRows);
+    const ryuProjects = parseRyuGraphProjects(projectRows);
     const ryuRelations = [
       ...parseRyuGraphRelations(constrainsRows, "CONSTRAINS", "note"),
       ...parseRyuGraphRelations(implementsRows, "IMPLEMENTS", "note"),
-      ...parseRyuGraphRelations(supersedesRows, "SUPERSEDES", "note")
+      ...parseRyuGraphRelations(supersedesRows, "SUPERSEDES", "note"),
+      ...parseRyuGraphRelations(definesRows, "DEFINES", "note"),
+      ...parseRyuGraphRelations(callsRows, "CALLS", "call_type"),
+      ...parseRyuGraphRelations(importsRows, "IMPORTS", "import_name"),
+      ...parseRyuGraphRelations(callsSqlRows, "CALLS_SQL", "note"),
+      ...parseRyuGraphRelations(usesConfigKeyRows, "USES_CONFIG_KEY", "note"),
+      ...parseRyuGraphRelations(usesResourceKeyRows, "USES_RESOURCE_KEY", "note"),
+      ...parseRyuGraphRelations(usesSettingKeyRows, "USES_SETTING_KEY", "note"),
+      ...parseRyuGraphRelations(containsRows, "CONTAINS", "note"),
+      ...parseRyuGraphRelations(containsModuleRows, "CONTAINS_MODULE", "note"),
+      ...parseRyuGraphRelations(exportsRows, "EXPORTS", "note"),
+      ...parseRyuGraphRelations(includesFileRows, "INCLUDES_FILE", "note"),
+      ...parseRyuGraphRelations(referencesProjectRows, "REFERENCES_PROJECT", "note"),
+      ...parseRyuGraphRelations(usesResourceRows, "USES_RESOURCE", "note"),
+      ...parseRyuGraphRelations(usesSettingRows, "USES_SETTING", "note"),
+      ...parseRyuGraphRelations(usesConfigRows, "USES_CONFIG", "note"),
+      ...parseRyuGraphRelations(transformsConfigRows, "TRANSFORMS_CONFIG", "note")
     ];
 
     return {
@@ -717,7 +834,11 @@ export async function loadContextData(): Promise<ContextData> {
       adrs: ryuAdrs.length > 0 ? ryuAdrs : cachedAdrs,
       rules: ryuRules.length > 0 ? ryuRules : cachedRules,
       chunks: ryuChunks.length > 0 ? ryuChunks : cachedChunks,
-      relations: ryuRelations.length > 0 ? [...ryuRelations, ...cachedChunkRelations] : cachedRelations,
+      modules: ryuModules.length > 0 ? ryuModules : cachedModules,
+      projects: ryuProjects.length > 0 ? ryuProjects : cachedProjects,
+      // Ryu now queries all relation types (core + chunk + module), so no need
+      // to merge cached chunk/module relations separately.
+      relations: ryuRelations.length > 0 ? ryuRelations : cachedRelations,
       ranking,
       source: "ryu"
     };
@@ -732,6 +853,8 @@ export async function loadContextData(): Promise<ContextData> {
       adrs: cachedAdrs,
       rules: cachedRules,
       chunks: cachedChunks,
+      modules: cachedModules,
+      projects: cachedProjects,
       relations: cachedRelations,
       ranking,
       source: "cache",

package/scaffold/mcp/src/graphMetrics.ts

@@ -0,0 +1,12 @@
+import type { RelationRecord } from "./types.js";
+
+export function relationDegree(relations: RelationRecord[]): Map<string, number> {
+  const degrees = new Map<string, number>();
+
+  for (const relation of relations) {
+    degrees.set(relation.from, (degrees.get(relation.from) ?? 0) + 1);
+    degrees.set(relation.to, (degrees.get(relation.to) ?? 0) + 1);
+  }
+
+  return degrees;
+}