fix(doctor): eliminate false warnings after clean-room bd init

Addresses remaining doctor warnings that fire after bd init in a fresh
git repo (PR gastownhall#1915 scope):

- CheckGitUpstream: skip warning when no remotes exist (cannot have
  upstream without a remote)
- bd init: auto-stage .beads/, AGENTS.md, .gitignore and commit so
  doctor does not warn about dirty working tree or untracked files
- bd init: clean noms LOCK files after store close and after git
  commit (pre-commit hook may reopen the database)
- store.Close: remove 0-byte noms LOCK files on shutdown

Co-authored-by: matt wilkie <maphew@gmail.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Executed-By: beads/crew/lizzy
Rig: beads
Role: crew

Author: steveyegge

cmd/bd/init.go

@@ -540,6 +540,9 @@ environment variable.`,
 			fmt.Fprintf(os.Stderr, "Warning: failed to close database: %v\n", err)
 		}
 
+		// Clean up 0-byte noms LOCK files left behind by the store open/close cycle.
+		dolt.CleanStaleNomsLocks(doltserver.ResolveDoltDir(beadsDir))
+
 		// Fork detection: offer to configure .git/info/exclude (GH#742)
 		setupExclude, _ := cmd.Flags().GetBool("setup-exclude")
 		if setupExclude {
@@ -624,6 +627,36 @@ environment variable.`,
 			addAgentsInstructions(!quiet, agentsTemplate)
 		}
 
+		// Auto-stage and commit beads files so bd doctor doesn't warn about
+		// untracked files or dirty working tree in a clean room setup.
+		// Only runs when not stealth, in a git repo, and using local storage.
+		if !stealth && isGitRepo() && useLocalBeads {
+			gitAddCmd := exec.Command("git", "add", ".beads/")
+			if _, addErr := gitAddCmd.CombinedOutput(); addErr == nil {
+				// Also stage AGENTS.md if it exists
+				if _, statErr := os.Stat("AGENTS.md"); statErr == nil {
+					agentsCmd := exec.Command("git", "add", "AGENTS.md")
+					_ = agentsCmd.Run()
+				}
+				// Also stage .gitignore if modified by EnsureProjectGitignore
+				if _, statErr := os.Stat(".gitignore"); statErr == nil {
+					giCmd := exec.Command("git", "add", ".gitignore")
+					_ = giCmd.Run()
+				}
+				commitCmd := exec.Command("git", "commit", "-m", "bd init: initialize beads issue tracking")
+				if commitOut, commitErr := commitCmd.CombinedOutput(); commitErr != nil {
+					if !quiet && !strings.Contains(string(commitOut), "nothing to commit") {
+						fmt.Fprintf(os.Stderr, "Warning: failed to commit beads files: %v\n", commitErr)
+					}
+				} else if !quiet {
+					fmt.Printf("  %s Committed beads files to git\n", ui.RenderPass("✓"))
+				}
+				// Clean up LOCK files again — the pre-commit hook may have
+				// reopened the database and left a new LOCK behind.
+				dolt.CleanStaleNomsLocks(doltserver.ResolveDoltDir(beadsDir))
+			}
+		}
+
 		// Check for missing git upstream and warn if not configured.
 		// Only warn when remotes exist (has origin but no upstream).
 		// Skip for brand-new repos with no remotes — the warning is noise there.

internal/storage/dolt/store.go

@@ -886,7 +886,8 @@ func isOnlyComments(stmt string) bool {
 	return true
 }
 
-// Close closes the database connection
+// Close closes the database connection and removes any 0-byte noms LOCK files
+// left behind by the embedded Dolt engine.
 func (s *DoltStore) Close() error {
 	s.closed.Store(true)
 	s.mu.Lock()
@@ -901,9 +902,40 @@ func (s *DoltStore) Close() error {
 		}
 	}
 	s.db = nil
+
+	// Clean up 0-byte noms LOCK files. The Dolt engine creates these when
+	// opening a database; they should be removed on clean shutdown but may
+	// persist after crashes or when bd init triggers hook reopens.
+	if s.dbPath != "" {
+		cleanZeroByteNomsLocks(s.dbPath)
+	}
+
 	return err
 }
 
+// cleanZeroByteNomsLocks removes 0-byte noms LOCK files from all databases
+// under doltDir. Only empty LOCK files are removed — non-empty ones may
+// indicate an active lock held by a running server.
+func cleanZeroByteNomsLocks(doltDir string) {
+	entries, err := os.ReadDir(doltDir)
+	if err != nil {
+		return
+	}
+	for _, entry := range entries {
+		if !entry.IsDir() {
+			continue
+		}
+		lockPath := filepath.Join(doltDir, entry.Name(), ".dolt", "noms", "LOCK")
+		info, statErr := os.Stat(lockPath)
+		if statErr != nil {
+			continue
+		}
+		if info.Size() == 0 {
+			_ = os.Remove(lockPath)
+		}
+	}
+}
+
 // Path returns the database directory path
 func (s *DoltStore) Path() string {
 	return s.dbPath