Clean up stale references to deleted directive files

Remove /refresh-directives references from save, checkpoint, scc, sync
commands. Trim sync.md from 400+ lines to essentials.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

.claude/commands/checkpoint.md

@@ -40,15 +40,6 @@ Please create a comprehensive git checkpoint with the following steps:
    - Confirm git commit succeeded by running `git log -1`
    - Report commit status to user
 
-## Part 3: Refresh Directives (MANDATORY)
-
-7. **Refresh directives** (MANDATORY):
-   - After checkpoint completion, auto-invoke `/refresh-directives`
-   - Re-read `directives.md` to prevent shortcut-taking
-   - Perform self-assessment for any violations
-   - Confirm commitment to agent coordination rules
-   - Report directives refreshed to user
-
 ## Benefits of Git Checkpoint
 
 **Git Checkpoint provides:**