fix(daemon): detect external db file replacement

When git merge replaces the .beads/beads.db file, the daemon's
SQLite connection becomes stale (still reading deleted inode).
This adds FreshnessChecker that detects file replacement via
inode/mtime comparison and triggers automatic reconnection.

Implementation:
- freshness.go: monitors db file for replacement
- store.go: adds EnableFreshnessChecking() and reconnect()
- queries.go: calls checkFreshness() on GetIssue/SearchIssues
- daemon.go: enables freshness checking at startup
- freshness_test.go: comprehensive tests including merge scenario

Code quality (per review):
- Extract configureConnectionPool() helper to reduce duplication
- Handle Close() error in reconnect() (log but continue)
- Use t.Cleanup() pattern in tests per project conventions
- Rename setupFreshnessTest() per naming conventions

Overhead: ~2.6μs per read op (~0.8% of total query time)

Signed-off-by: Alessandro De Blasis <alex@deblasis.net>

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

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

internal/storage/sqlite/queries.go

@@ -166,6 +166,9 @@ func (s *SQLiteStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 
 // GetIssue retrieves an issue by ID
 func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue, error) {
+	// Check for external database file modifications (daemon mode)
+	s.checkFreshness()
+
 	var issue types.Issue
 	var closedAt sql.NullTime
 	var estimatedMinutes sql.NullInt64
@@ -1305,6 +1308,9 @@ func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, tx *sql.
 
 // SearchIssues finds issues matching query and filters
 func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter types.IssueFilter) ([]*types.Issue, error) {
+	// Check for external database file modifications (daemon mode)
+	s.checkFreshness()
+
 	whereClauses := []string{}
 	args := []interface{}{}