chore(ci): fix pre-commit hook failures

Fix JSON syntax errors in .devcontainer/devcontainer.json (removed
invalid JS-style // comments) and .devcontainer/opencode.json (removed
90+ trailing commas). Apply auto-fixes for end-of-file and trailing
whitespace issues across 100+ files. Fix SIM105 ruff violations in
benchmarks/core_circuit_breaker_bench.py (use contextlib.suppress).

Note: The security fix from issue #7478 (validate_path startswith bypass)
was already delivered to master in commit e18ac5f2. This PR as currently
structured is non-atomic (35 commits across 10+ issues) and needs
significant restructure before merge. This commit only addresses the
CI/pre-commit failures.

ISSUES CLOSED: #7478

docs/development/agent-system-specification.md

@@ -76,7 +76,7 @@ blockdiag {
     label = "Tier 2: Workers";
     color = "#FCE4EC";
     "Implementation Worker\n(issue-impl mode)" [color = "#C62828", textcolor = "#fff"];
-  
+
     "PR Reviewer" [color = "#C62828", textcolor = "#fff"];
     "UAT Worker" [color = "#C62828", textcolor = "#fff"];
     "Bug Hunter Worker" [color = "#C62828", textcolor = "#fff"];
@@ -3379,10 +3379,10 @@ FG --> BGR : cleanup old tickets
 note bottom of FG
   Tracking issues follow format:
   [PREFIX] Type (Cycle N)
-  
+
   Announcements follow format:
   [PREFIX] Announce: message
-  
+
   ALL carry "Automation Tracking" label
 end note
 @enduml

docs/development/automation-tracking.md

@@ -240,7 +240,7 @@ for issue in automation_tracking_issues:
         expected_interval = get_expected_interval(issue.agent_prefix, issue.type)
         time_since_creation = now() - issue.created_at
         staleness_threshold = expected_interval * 1.2  # 20% tolerance
-        
+
         if time_since_creation > staleness_threshold:
             mark_agent_as_stalled(issue.agent_prefix)
             trigger_recovery_actions(issue.agent_prefix, issue)