feat(skills): add dryRun flag for scan prune path

Add a `dryRun` option to the scan-projects endpoint. When true, the
scan identifies which skills would be pruned and which agents would be
affected, but does not delete anything or modify agent configs.

The response now includes:
- `pruned[]`: list of skills that would be (or were) removed, with
  affected agent names
- `dryRun`: boolean echoed back so callers can distinguish preview
  results from live mutations

This lets callers preview destructive prune operations before committing
to them, addressing the review concern about silent deletion of
production data.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

server/src/__tests__/company-skills-prune.test.ts

@@ -282,4 +282,46 @@ describeEmbeddedPostgres("scanProjectWorkspaces prune path", () => {
       ]),
     );
   });
+
+  it("reports pruned skills without deleting when dryRun is true", async () => {
+    stubGitHubSource(["keep-skill"]);
+
+    const { companySkillService } = await import("../services/company-skills.js");
+    const svc = companySkillService(db);
+    const result = await svc.scanProjectWorkspaces(companyId, { dryRun: true });
+
+    // The result should flag dryRun and list what would be pruned
+    expect(result.dryRun).toBe(true);
+    expect(result.pruned).toEqual(
+      expect.arrayContaining([
+        expect.objectContaining({
+          slug: "prune-skill",
+          affectedAgents: expect.arrayContaining(["Builder"]),
+        }),
+      ]),
+    );
+
+    // No warnings emitted (nothing was actually deleted)
+    const pruneWarnings = result.warnings.filter((w) => w.includes("prune-skill"));
+    expect(pruneWarnings).toHaveLength(0);
+
+    // Both skills should still exist in the database
+    const remaining = await db
+      .select()
+      .from(companySkills)
+      .where(eq(companySkills.companyId, companyId));
+    const remainingSlugs = remaining.map((r) => r.slug);
+    expect(remainingSlugs).toContain("keep-skill");
+    expect(remainingSlugs).toContain("prune-skill");
+
+    // Agent config should be unchanged
+    const [agentRow] = await db
+      .select()
+      .from(agents)
+      .where(eq(agents.id, agentId));
+    const config = agentRow!.adapterConfig as Record<string, unknown>;
+    const syncConfig = config.paperclipSkillSync as Record<string, unknown>;
+    const desiredSkills = syncConfig.desiredSkills as string[];
+    expect(desiredSkills).toContain("test-org/test-skills/prune-skill");
+  });
 });