Fix bd init to auto-import issues from git on fresh clone

Prevents agents from creating duplicate low-numbered issues when starting
with a fresh git clone that already has issues.jsonl in git history.

Changes:
- bd init now checks for existing issues in git after DB creation
- Auto-imports with collision resolution if found
- Updates AGENTS.md to simplify onboarding (just 'bd init')

Fixes the scenario where:
1. Fresh clone has .beads/issues.jsonl in git (212 issues)
2. Agent runs bd init (creates empty DB)
3. Agent starts creating bd-1, bd-2, etc (collisions with git)

Now bd init automatically imports all issues from git on first run.

Amp-Thread-ID: https://ampcode.com/threads/T-8a41f14d-d4c3-4c50-a18b-5f112110f138
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -456,11 +456,9 @@ Happy coding! 🔗
 
 ### Quick Start
 
-**FIRST TIME?** Import existing issues from git:
+**FIRST TIME?** Just run `bd init` - it auto-imports issues from git:
 ```bash
-bd import -i .beads/issues.jsonl --json
-# Or if issues.jsonl is empty in working tree but exists in git:
-git show HEAD:.beads/issues.jsonl | bd import -i /dev/stdin --json
+bd init --prefix bd
 ```
 
 **Check for ready work:**

cmd/bd/autoimport.go

@@ -43,7 +43,7 @@ func checkAndAutoImport(ctx context.Context, store storage.Storage) bool {
 	}
 
 	// Import from git
-	if err := importFromGit(ctx, store, jsonlPath); err != nil {
+	if err := importFromGit(ctx, dbPath, store, jsonlPath); err != nil {
 		if !jsonOutput {
 			fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
 			fmt.Fprintf(os.Stderr, "Try manually: git show HEAD:%s | bd import -i /dev/stdin\n", jsonlPath)
@@ -130,7 +130,7 @@ func findGitRoot() string {
 }
 
 // importFromGit imports issues from git HEAD
-func importFromGit(ctx context.Context, store storage.Storage, jsonlPath string) error {
+func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage, jsonlPath string) error {
 	// Get content from git
 	cmd := exec.Command("git", "show", fmt.Sprintf("HEAD:%s", jsonlPath))
 	jsonlData, err := cmd.Output()
@@ -167,6 +167,6 @@ func importFromGit(ctx context.Context, store storage.Storage, jsonlPath string)
 		SkipPrefixValidation: true, // Auto-import is lenient about prefixes
 	}
 
-	_, err = importIssuesCore(ctx, dbPath, store, issues, opts)
+	_, err = importIssuesCore(ctx, dbFilePath, store, issues, opts)
 	return err
 }

cmd/bd/init.go

@@ -85,18 +85,36 @@ bd.db
 
 		// Store the bd version in metadata (for version mismatch detection)
 		if err := store.SetMetadata(ctx, "bd_version", Version); err != nil {
-			fmt.Fprintf(os.Stderr, "Warning: failed to store version metadata: %v\n", err)
-			// Non-fatal - continue anyway
+		fmt.Fprintf(os.Stderr, "Warning: failed to store version metadata: %v\n", err)
+		// Non-fatal - continue anyway
 		}
 
-		if err := store.Close(); err != nil {
-			fmt.Fprintf(os.Stderr, "Warning: failed to close database: %v\n", err)
+		// Check if git has existing issues to import (fresh clone scenario)
+		issueCount, jsonlPath := checkGitForIssues()
+		if issueCount > 0 {
+		if !quiet {
+		fmt.Fprintf(os.Stderr, "\n✓ Database initialized. Found %d issues in git, importing...\n", issueCount)
 		}
+		
+		if err := importFromGit(ctx, dbPath, store, jsonlPath); err != nil {
+			if !quiet {
+				fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
+				fmt.Fprintf(os.Stderr, "Try manually: git show HEAD:%s | bd import -i /dev/stdin\n", jsonlPath)
+			}
+			// Non-fatal - continue with empty database
+		} else if !quiet {
+			fmt.Fprintf(os.Stderr, "✓ Successfully imported %d issues from git.\n\n", issueCount)
+		}
+	}
 
-		// Skip output if quiet mode
-		if quiet {
-			return
-		}
+	if err := store.Close(); err != nil {
+		fmt.Fprintf(os.Stderr, "Warning: failed to close database: %v\n", err)
+	}
+
+	// Skip output if quiet mode
+	if quiet {
+		return
+	}
 
 		green := color.New(color.FgGreen).SprintFunc()
 		cyan := color.New(color.FgCyan).SprintFunc()