diff --git a/server/src/app.ts b/server/src/app.ts
index e55edcf0..d5e9818f 100644
--- a/server/src/app.ts
+++ b/server/src/app.ts
@@ -152,8 +152,8 @@ export async function createApp(
   );
   api.use("/companies", companyRoutes(db, opts.storageService));
   api.use(companySkillRoutes(db));
-  api.use(skillRegistryRoutes());
-  api.use(skillGroupRoutes());
+  api.use(skillRegistryRoutes(db));
+  api.use(skillGroupRoutes(db));
   api.use(agentRoutes(db));
   api.use(assetRoutes(db, opts.storageService));
   api.use(projectRoutes(db));
diff --git a/server/src/routes/skill-registry-groups.ts b/server/src/routes/skill-registry-groups.ts
index f16f88c7..2e9ea72f 100644
--- a/server/src/routes/skill-registry-groups.ts
+++ b/server/src/routes/skill-registry-groups.ts
@@ -1,21 +1,37 @@
 import { Router } from "express";
 import os from "node:os";
-import path from "node:path";
+import type { Db } from "@paperclipai/db";
+import { agentService } from "../services/agents.js";
+import { resolveAdapterSkillConfig } from "@paperclipai/adapter-utils";
 import { skillGroupService } from "../services/skill-registry-groups.js";
+import { skillRegistryService } from "../services/skill-registry.js";
 import { assertBoard } from "./authz.js";
 
-/** Default skills directory when client doesn't provide one */
-function defaultSkillsDir(): string {
-  return path.join(os.homedir(), ".claude", "skills");
+/**
+ * Resolves the agentSkillsDir for a given agentId by looking up the agent's
+ * adapter type and calling resolveAdapterSkillConfig. Throws with a status
+ * property so route handlers can forward the correct HTTP status code.
+ */
+async function resolveSkillsDirForAgent(db: Db, agentId: string): Promise<string> {
+  const agent = await agentService(db).getById(agentId);
+  if (!agent) throw Object.assign(new Error("Agent not found"), { status: 404 });
+  const config = resolveAdapterSkillConfig(agent.adapterType);
+  if (!config.supportsInstall || !config.skillDir) {
+    throw Object.assign(
+      new Error(config.unsupportedReason ?? "Adapter does not support skill install"),
+      { status: 422 },
+    );
+  }
+  return config.skillDir.replace(/^~/, os.homedir());
 }
 
 /**
  * REST routes for skill groups.
  *
- * Note: does NOT take a db param — skill groups use the libSQL registry.db.
+ * Accepts a db param for agent lookup (to resolve adapter-based skill directories).
  * All route handlers assert `board` access before delegating to skillGroupService.
  */
-export function skillGroupRoutes(): Router {
+export function skillGroupRoutes(db: Db): Router {
   const router = Router();
   const svc = skillGroupService();
 
@@ -168,37 +184,51 @@ export function skillGroupRoutes(): Router {
     }
   });
 
+  // Assign a group to an agent — resolves skill dir from agentId URL param server-side
   router.post("/skill-registry/agents/:agentId/groups", async (req, res) => {
     assertBoard(req);
     try {
-      const { groupId, agentSkillsDir } = req.body as { groupId?: string; agentSkillsDir?: string };
+      const { groupId } = req.body as { groupId?: string };
       if (!groupId) {
         return res.status(400).json({ error: "groupId required" });
       }
-      const resolvedDir = agentSkillsDir || defaultSkillsDir();
-      const result = await svc.assignGroup(groupId, req.params.agentId, resolvedDir);
+      const agentSkillsDir = await resolveSkillsDirForAgent(db, req.params.agentId);
+      const result = await svc.assignGroup(groupId, req.params.agentId, agentSkillsDir);
       res.status(201).json(result);
-    } catch (err) {
-      handleError(res, err);
+    } catch (err: any) {
+      const status = err.status ?? 500;
+      return res.status(status).json({ error: err.message });
     }
   });
 
+  // Remove a group from an agent — resolves skill dir from agentId URL param server-side
   router.delete("/skill-registry/agents/:agentId/groups/:groupId(*)", async (req, res) => {
     assertBoard(req);
     try {
-      const { agentSkillsDir } = req.body as { agentSkillsDir?: string };
-      const resolvedDir = agentSkillsDir || defaultSkillsDir();
-      await svc.removeGroup(req.params.groupId, req.params.agentId, resolvedDir);
+      const agentSkillsDir = await resolveSkillsDirForAgent(db, req.params.agentId);
+      await svc.removeGroup(req.params.groupId, req.params.agentId, agentSkillsDir);
       res.status(204).end();
-    } catch (err) {
-      handleError(res, err);
+    } catch (err: any) {
+      const status = err.status ?? 500;
+      return res.status(status).json({ error: err.message });
     }
   });
 
+  // List installed skills for an agent.
+  // For hermes_local agents, syncs native skills before returning the list.
   router.get("/skill-registry/agents/:agentId/skills", async (req, res) => {
     assertBoard(req);
     try {
-      const skills = await svc.listAgentSkills(req.params.agentId);
+      const agentId = req.params.agentId;
+      const agent = await agentService(db).getById(agentId);
+      if (!agent) {
+        return res.status(404).json({ error: "Agent not found" });
+      }
+      if (agent.adapterType === "hermes_local") {
+        const registrySvc = skillRegistryService();
+        await registrySvc.syncHermesNativeSkills(agentId);
+      }
+      const skills = await svc.listAgentSkills(agentId);
       res.json(skills);
     } catch (err) {
       handleError(res, err);
diff --git a/server/src/routes/skill-registry.ts b/server/src/routes/skill-registry.ts
index d92f9871..71d4f479 100644
--- a/server/src/routes/skill-registry.ts
+++ b/server/src/routes/skill-registry.ts
@@ -1,15 +1,40 @@
 import { Router } from "express";
+import os from "node:os";
+import { and, eq } from "drizzle-orm";
+import type { Db } from "@paperclipai/db";
+import { agentService } from "../services/agents.js";
+import { resolveAdapterSkillConfig } from "@paperclipai/adapter-utils";
 import { skillRegistryService } from "../services/skill-registry.js";
 import { skillRatingService } from "../services/skill-registry-ratings.js";
+import { getSkillRegistryDb } from "../services/skill-registry-db.js";
+import { agentSkills } from "../services/skill-registry-schema.js";
 import { assertBoard } from "./authz.js";
 
+/**
+ * Resolves the agentSkillsDir for a given agentId by looking up the agent's
+ * adapter type and calling resolveAdapterSkillConfig. Throws with a status
+ * property so route handlers can forward the correct HTTP status code.
+ */
+async function resolveSkillsDirForAgent(db: Db, agentId: string): Promise<string> {
+  const agent = await agentService(db).getById(agentId);
+  if (!agent) throw Object.assign(new Error("Agent not found"), { status: 404 });
+  const config = resolveAdapterSkillConfig(agent.adapterType);
+  if (!config.supportsInstall || !config.skillDir) {
+    throw Object.assign(
+      new Error(config.unsupportedReason ?? "Adapter does not support skill install"),
+      { status: 422 },
+    );
+  }
+  return config.skillDir.replace(/^~/, os.homedir());
+}
+
 /**
  * REST routes for the skill registry.
  *
- * Note: does NOT take a db param — the skill registry manages its own libSQL database.
+ * Accepts a db param for agent lookup (to resolve adapter-based skill directories).
  * All route handlers assert `board` access before delegating to skillRegistryService.
  */
-export function skillRegistryRoutes(): Router {
+export function skillRegistryRoutes(db: Db): Router {
   const router = Router();
   const svc = skillRegistryService();
 
@@ -30,36 +55,68 @@ export function skillRegistryRoutes(): Router {
     res.json(versions);
   });
 
-  // Install skill to agent directory
+  // Install skill to agent directory — resolves path from agentId server-side
   router.post("/skill-registry/skills/:sourceId/:slug/install", async (req, res) => {
     assertBoard(req);
     const skillId = `${req.params.sourceId}/${req.params.slug}`;
-    const { agentSkillsDir } = req.body as { agentSkillsDir: string };
-    if (!agentSkillsDir) return res.status(400).json({ error: "agentSkillsDir required" });
-    const result = await svc.install(skillId, agentSkillsDir);
-    res.json(result);
+    const { agentId } = req.body as { agentId: string };
+    if (!agentId) return res.status(400).json({ error: "agentId required" });
+    try {
+      const agentSkillsDir = await resolveSkillsDirForAgent(db, agentId);
+      const result = await svc.install(skillId, agentSkillsDir);
+      res.json(result);
+    } catch (err: any) {
+      const status = err.status ?? 500;
+      return res.status(status).json({ error: err.message });
+    }
   });
 
-  // Rollback to a specific version
+  // Rollback to a specific version — resolves path from agentId server-side
   router.post("/skill-registry/skills/:sourceId/:slug/rollback", async (req, res) => {
     assertBoard(req);
     const skillId = `${req.params.sourceId}/${req.params.slug}`;
-    const { versionId, agentSkillsDir } = req.body as { versionId: string; agentSkillsDir: string };
-    if (!versionId || !agentSkillsDir) {
-      return res.status(400).json({ error: "versionId and agentSkillsDir required" });
+    const { versionId, agentId } = req.body as { versionId: string; agentId: string };
+    if (!versionId || !agentId) {
+      return res.status(400).json({ error: "versionId and agentId required" });
+    }
+    try {
+      const agentSkillsDir = await resolveSkillsDirForAgent(db, agentId);
+      await svc.rollback(skillId, versionId, agentSkillsDir);
+      res.json({ ok: true });
+    } catch (err: any) {
+      const status = err.status ?? 500;
+      return res.status(status).json({ error: err.message });
     }
-    await svc.rollback(skillId, versionId, agentSkillsDir);
-    res.json({ ok: true });
   });
 
-  // 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
+  // Soft-delete a skill (also removes files from disk).
+  // agentId is passed as a query param (DELETE semantics — no body).
+  // Returns 403 if the skill is a native skill (source === 'native').
   router.delete("/skill-registry/skills/:sourceId/:slug", async (req, res) => {
     assertBoard(req);
     const skillId = `${req.params.sourceId}/${req.params.slug}`;
-    const agentSkillsDir = (req.query.agentSkillsDir as string | undefined) ?? "";
-    await svc.uninstall(skillId, agentSkillsDir);
-    res.json({ ok: true });
+    const agentId = req.query.agentId as string | undefined;
+    if (!agentId) return res.status(400).json({ error: "agentId required" });
+
+    // Check native skill protection
+    const registryDb = await getSkillRegistryDb();
+    const agentSkillRows = await registryDb
+      .select()
+      .from(agentSkills)
+      .where(and(eq(agentSkills.skillId, skillId), eq(agentSkills.agentId, agentId)));
+    const agentSkillRow = agentSkillRows[0];
+    if (agentSkillRow?.source === "native") {
+      return res.status(403).json({ error: "Cannot remove native skills" });
+    }
+
+    try {
+      const agentSkillsDir = await resolveSkillsDirForAgent(db, agentId);
+      await svc.uninstall(skillId, agentSkillsDir);
+      res.json({ ok: true });
+    } catch (err: any) {
+      const status = err.status ?? 500;
+      return res.status(status).json({ error: err.message });
+    }
   });
 
   // Submit a personal rating for a skill