fix(skills): emit warning for all pruned skills, not just agent-attached ones

Previously, skills pruned during re-scan only emitted a warning when
they were attached to agents. Skills with no agent references were
deleted silently. Now every pruned skill emits a warning in the scan
result so the deletion is always visible to the caller.

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

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

@@ -250,7 +250,10 @@ describeEmbeddedPostgres("scanProjectWorkspaces prune path", () => {
     expect(remainingSlugs).toContain("keep-skill");
     expect(remainingSlugs).not.toContain("prune-skill");
 
-    // No warnings about agent detachment since no agents used it
+    // A deletion warning should still be emitted (no detachment, but deletion is confirmed)
+    const deleteWarnings = result.warnings.filter((w) => w.includes("prune-skill") && w.includes("deleted"));
+    expect(deleteWarnings).toHaveLength(1);
+    // No agent-detachment warning since no agents used it
     const detachWarnings = result.warnings.filter((w) => w.includes("prune-skill") && w.includes("detached"));
     expect(detachWarnings).toHaveLength(0);
   });

server/src/services/company-skills.ts

@@ -2061,6 +2061,10 @@ export function companySkillService(db: Db) {
             warnings.push(
               `Skill "${skill.slug}" was removed from ${sourceLocator} and detached from ${usedByAgents.map((a) => a.name).join(", ")}.`,
             );
+          } else {
+            warnings.push(
+              `Skill "${skill.slug}" was removed from ${sourceLocator} and deleted.`,
+            );
           }
           await deleteSkill(companyId, skill.id);
         }