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/nodb_test.go

@@ -219,6 +219,9 @@ func TestInitializeNoDbMode_SetsStoreActive(t *testing.T) {
 	// The bug was that initializeNoDbMode() set `store` but not `storeActive`,
 	// so ensureStoreActive() would try to find a SQLite database.
 
+	// Reset global state for test isolation
+	ensureCleanGlobalState(t)
+
 	tempDir := t.TempDir()
 	beadsDir := filepath.Join(tempDir, ".beads")
 	if err := os.MkdirAll(beadsDir, 0o755); err != nil {