[nexus] feat(19-01): adapter-aware skill service layer — source column, uninstall file removal, syncHermesNativeSkills

- agentSkills schema gets source TEXT NOT NULL DEFAULT 'managed' column
- Migration guard in getSkillRegistryDb() handles existing DBs via ALTER TABLE
- uninstall() now accepts agentSkillsDir and removes files before soft-deleting
- syncHermesNativeSkills() reads ~/.hermes/skills/, creates stub rows with source='native'
- listAgentSkills() returns typed objects {skillId, source, installedAt} not string[]
- Interim uninstall route fix: reads agentSkillsDir from query param until Plan 02 wires agentId

server/src/routes/skill-registry.ts

@@ -52,11 +52,13 @@ export function skillRegistryRoutes(): Router {
     res.json({ ok: true });
   });
 
-  // Soft-delete a skill
+  // Soft-delete a skill (also removes files from disk)
+  // agentSkillsDir is required as a query param until Plan 02 replaces it with agentId-based resolution
   router.delete("/skill-registry/skills/:sourceId/:slug", async (req, res) => {
     assertBoard(req);
     const skillId = `${req.params.sourceId}/${req.params.slug}`;
-    await svc.uninstall(skillId);
+    const agentSkillsDir = (req.query.agentSkillsDir as string | undefined) ?? "";
+    await svc.uninstall(skillId, agentSkillsDir);
     res.json({ ok: true });
   });
 

server/src/services/skill-registry-db.ts

@@ -166,6 +166,7 @@ export async function getSkillRegistryDb(): Promise<SkillRegistryDb> {
     `ALTER TABLE agent_skills ADD COLUMN task_count INTEGER NOT NULL DEFAULT 0`,
     `ALTER TABLE agent_skills ADD COLUMN avg_cost_usd REAL`,
     `ALTER TABLE agent_skills ADD COLUMN last_used_at INTEGER`,
+    `ALTER TABLE agent_skills ADD COLUMN source TEXT NOT NULL DEFAULT 'managed'`,
   ];
   for (const sql of agentSkillsAlters) {
     try {

server/src/services/skill-registry-groups.ts

@@ -419,13 +419,21 @@ export function skillGroupService() {
         .where(inArray(skillGroups.id, groupIds));
     },
 
-    async listAgentSkills(agentId: string): Promise<string[]> {
+    async listAgentSkills(agentId: string): Promise<Array<{ skillId: string; source: "managed" | "native"; installedAt: number }>> {
       const db = await getSkillRegistryDb();
       const rows = await db
-        .select()
+        .select({
+          skillId: agentSkills.skillId,
+          source: agentSkills.source,
+          installedAt: agentSkills.installedAt,
+        })
         .from(agentSkills)
         .where(eq(agentSkills.agentId, agentId));
-      return rows.map((r) => r.skillId);
+      return rows.map((r) => ({
+        skillId: r.skillId,
+        source: (r.source ?? "managed") as "managed" | "native",
+        installedAt: r.installedAt,
+      }));
     },
 
     async getAgentEffectiveSkills(agentId: string): Promise<string[]> {

server/src/services/skill-registry-schema.ts

@@ -73,6 +73,7 @@ export const agentSkills = sqliteTable("agent_skills", {
   agentId: text("agent_id").notNull(),
   skillId: text("skill_id").notNull(),
   installedAt: integer("installed_at").notNull(),
+  source: text("source").notNull().default("managed"), // 'managed' | 'native'
   taskCount: integer("task_count").notNull().default(0),
   avgCostUsd: real("avg_cost_usd"),
   lastUsedAt: integer("last_used_at"),

server/src/services/skill-registry.ts

@@ -1,6 +1,7 @@
 import { eq, isNull, and, desc, sql } from "drizzle-orm";
-import { cp, mkdir, rm } from "node:fs/promises";
+import { cp, mkdir, rm, readdir } from "node:fs/promises";
 import path from "node:path";
+import os from "node:os";
 import { getSkillRegistryDb } from "./skill-registry-db.js";
 import { skills, skillVersions, skillFiles, communityRatings, agentSkills } from "./skill-registry-schema.js";
 import { fetchAllSources, type SkillSourceConfig } from "./skill-registry-fetcher.js";
@@ -160,8 +161,14 @@ export function skillRegistryService() {
       };
     },
 
-    async uninstall(skillId: string): Promise<void> {
+    async uninstall(skillId: string, agentSkillsDir: string): Promise<void> {
       const db = await getSkillRegistryDb();
+
+      // Remove skill files from disk before soft-deleting the registry row
+      const slug = skillId.split("/").pop() ?? skillId;
+      const targetDir = path.join(agentSkillsDir, slug);
+      await rm(targetDir, { recursive: true, force: true });
+
       await db
         .update(skills)
         .set({ removedAt: Date.now(), updatedAt: Date.now() })
@@ -193,6 +200,51 @@ export function skillRegistryService() {
         .where(eq(skills.id, skillId));
     },
 
+    /**
+     * Sync native Hermes skills from ~/.hermes/skills/ into the registry.
+     * Creates a minimal skills stub row and an agentSkills row with source='native'
+     * for each subdirectory found. Idempotent — safe to call multiple times.
+     * Returns silently if ~/.hermes/skills/ does not exist.
+     */
+    async syncHermesNativeSkills(agentId: string): Promise<void> {
+      const hermesSkillsDir = path.join(os.homedir(), ".hermes", "skills");
+      let entries: string[];
+      try {
+        entries = await readdir(hermesSkillsDir);
+      } catch {
+        // Directory doesn't exist — no native skills
+        return;
+      }
+
+      const db = await getSkillRegistryDb();
+      const now = Date.now();
+
+      for (const entry of entries) {
+        const skillId = `hermes-native/${entry}`;
+
+        // Create a minimal stub in the skills table so JOINs work
+        await db.insert(skills).values({
+          id: skillId,
+          sourceId: "hermes-native",
+          name: entry,
+          description: null,
+          sourceUrl: null,
+          activeVersionId: null,
+          removedAt: null,
+          createdAt: now,
+          updatedAt: now,
+        }).onConflictDoNothing();
+
+        // Record in agent_skills with source = 'native'
+        await db.insert(agentSkills).values({
+          agentId,
+          skillId,
+          installedAt: now,
+          source: "native",
+        }).onConflictDoNothing();
+      }
+    },
+
     async fetchAll(
       sources?: SkillSourceConfig[],
     ): Promise<{ fetched: number; errors: string[] }> {