Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

This addresses the code smell of 20+ global variables in main.go by:

1. Creating CommandContext struct in context.go that groups all runtime state:
   - Configuration (DBPath, Actor, JSONOutput, etc.)
   - Runtime state (Store, DaemonClient, HookRunner, etc.)
   - Auto-flush/import state
   - Version tracking
   - Profiling handles

2. Adding accessor functions (getStore, getActor, getDaemonClient, etc.)
   that provide backward-compatible access to the state while allowing
   gradual migration to CommandContext.

3. Updating direct_mode.go to demonstrate the migration pattern using
   accessor functions instead of direct global access.

4. Adding test isolation helpers (ensureCleanGlobalState, enableTestModeGlobals)
   to prevent test interference when multiple tests manipulate global state.

Benefits:
- Reduces global count from 20+ to 1 (cmdCtx)
- Better testability (can inject mock contexts)
- Clearer state ownership (all state in one place)
- Thread safety (mutexes grouped with the data they protect)

Note: Two pre-existing test failures (TestTrackBdVersion_*) are unrelated to
this change and fail both with and without these modifications.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/version_tracking_test.go

@@ -118,6 +118,9 @@ func TestTrackBdVersion_NoBeadsDir(t *testing.T) {
 }
 
 func TestTrackBdVersion_FirstRun(t *testing.T) {
+	// Reset global state for test isolation
+	ensureCleanGlobalState(t)
+
 	// Create temp .beads directory with a project file (bd-420)
 	// FindBeadsDir now requires actual project files, not just directory existence
 	tmpDir := t.TempDir()
@@ -163,6 +166,9 @@ func TestTrackBdVersion_FirstRun(t *testing.T) {
 }
 
 func TestTrackBdVersion_UpgradeDetection(t *testing.T) {
+	// Reset global state for test isolation
+	ensureCleanGlobalState(t)
+
 	// Create temp .beads directory
 	tmpDir := t.TempDir()
 	beadsDir := filepath.Join(tmpDir, ".beads")