fix(skills): scope skill-command APIs to respect agent allowlists (#32155)

* refactor(skills): use explicit skill-command scope APIs

* test(skills): cover scoped listing and telegram allowlist

* fix(skills): add mergeSkillFilters edge-case tests and simplify dead code

Cover unrestricted-co-tenant and empty-allowlist merge paths in
skill-commands tests. Remove dead ternary in bot-handlers pagination.
Add clarifying comments on undefined vs [] filter semantics.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* refactor(skills): collapse scope functions into single listSkillCommandsForAgents

Replace listSkillCommandsForAgentIds, listSkillCommandsForAllAgents, and
the deprecated listSkillCommandsForAgents with a single function that
accepts optional agentIds and falls back to all agents when omitted.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(skills): harden realpathSync race and add missing test coverage

- Wrap fs.realpathSync in try-catch to gracefully skip workspaces that
  disappear between existsSync and realpathSync (TOCTOU race).
- Log verbose diagnostics for missing/unresolvable workspace paths.
- Add test for overlapping allowlists deduplication on shared workspaces.
- Add test for graceful skip of missing workspaces.
- Add test for pagination callback without agent suffix (default agent).
- Clean up temp directories in skill-commands tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(telegram): warn when nativeSkillsEnabled but no agent route is bound

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: use runtime.log instead of nonexistent runtime.warn

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

src/telegram/bot-handlers.ts

@@ -1142,10 +1142,10 @@ export const registerTelegramHandlers = ({
           return;
         }
 
-        const agentId = paginationMatch[2]?.trim() || resolveDefaultAgentId(cfg) || undefined;
+        const agentId = paginationMatch[2]?.trim() || resolveDefaultAgentId(cfg);
         const skillCommands = listSkillCommandsForAgents({
           cfg,
-          agentIds: agentId ? [agentId] : undefined,
+          agentIds: [agentId],
         });
         const result = buildCommandsMessagePaginated(cfg, skillCommands, {
           page,