Add conflict marker detection to bd import/validate

- bd import now detects git conflict markers and shows resolution steps
- bd validate --checks=conflicts improved with clearer instructions
- Updated AGENTS.md with better conflict resolution docs
- Closes bd-7e7ddffa epic (repair tools complete)

Amp-Thread-ID: https://ampcode.com/threads/T-4a11a65b-56c2-4d92-8f68-66f0a56ab5e3
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -602,17 +602,27 @@ The daemon maintains its own view of the current working directory and git state
 **With hash-based IDs (v0.20.1+), ID collisions are eliminated!** Different issues get different hash IDs, so most git merges succeed cleanly.
 
 **When git merge conflicts occur:**
-Git conflicts in `.beads/beads.jsonl` happen when the same issue is modified on both branches (different timestamps/fields). This is a **same-issue update conflict**, not an ID collision.
+Git conflicts in `.beads/beads.jsonl` happen when the same issue is modified on both branches (different timestamps/fields). This is a **same-issue update conflict**, not an ID collision. Conflicts are rare in practice since hash IDs prevent structural collisions.
 
-**Resolution:**
+**Automatic detection:**
+bd automatically detects conflict markers (`<<<<<<<`, `=======`, `>>>>>>>`) and shows clear resolution steps:
+- `bd import` rejects files with conflict markers and shows resolution commands
+- `bd validate --checks=conflicts` scans for conflicts in JSONL
+
+**Resolution workflow:**
 ```bash
-# After git merge creates conflict
+# After git merge creates conflict in .beads/beads.jsonl
-git checkout --theirs .beads/beads.jsonl  # Accept remote version
-# OR
-git checkout --ours .beads/beads.jsonl    # Keep local version
-# OR manually resolve in editor
 
-# Import the resolved JSONL
+# Option 1: Accept their version (remote)
+git checkout --theirs .beads/beads.jsonl
+bd import -i .beads/beads.jsonl
+
+# Option 2: Keep our version (local)
+git checkout --ours .beads/beads.jsonl  
+bd import -i .beads/beads.jsonl
+
+# Option 3: Manual resolution in editor
+# Edit .beads/beads.jsonl to remove conflict markers
 bd import -i .beads/beads.jsonl
 
 # Commit the merge
@@ -620,7 +630,7 @@ git add .beads/beads.jsonl
 git commit
 ```
 
-**bd automatically handles updates** - same ID with different content is a normal update operation. No special flags needed.
+**Note:** `bd import` automatically handles updates - same ID with different content is a normal update operation. No special flags needed. If you accidentally modified the same issue in both branches, just pick whichever version is more complete.
 
 ### Advanced: Intelligent Merge Tools
 

cmd/bd/import.go

@@ -59,24 +59,34 @@ Behavior:
 		lineNum := 0
 
 		for scanner.Scan() {
-			lineNum++
+		lineNum++
-			line := scanner.Text()
+		line := scanner.Text()
 
-			// Skip empty lines
+		// Skip empty lines
-			if line == "" {
+		if line == "" {
-				continue
+		continue
-			}
-
-			// Parse JSON
-			var issue types.Issue
-			if err := json.Unmarshal([]byte(line), &issue); err != nil {
-				fmt.Fprintf(os.Stderr, "Error parsing line %d: %v\n", lineNum, err)
-				os.Exit(1)
-			}
-
-			allIssues = append(allIssues, &issue)
 		}
 
+		// Detect git conflict markers
+		if strings.Contains(line, "<<<<<<<") || strings.Contains(line, "=======") || strings.Contains(line, ">>>>>>>") {
+		 fmt.Fprintf(os.Stderr, "Error: Git conflict markers detected in JSONL file (line %d)\n\n", lineNum)
+		fmt.Fprintf(os.Stderr, "To resolve:\n")
+		fmt.Fprintf(os.Stderr, "  git checkout --ours .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n")
+		 fmt.Fprintf(os.Stderr, "  git checkout --theirs .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n\n")
+			fmt.Fprintf(os.Stderr, "For advanced field-level merging, see: https://github.com/neongreen/mono/tree/main/beads-merge\n")
+		 os.Exit(1)
+		 }
+
+		// Parse JSON
+		var issue types.Issue
+		if err := json.Unmarshal([]byte(line), &issue); err != nil {
+			fmt.Fprintf(os.Stderr, "Error parsing line %d: %v\n", lineNum, err)
+			os.Exit(1)
+		}
+
+		allIssues = append(allIssues, &issue)
+	}
+
 		if err := scanner.Err(); err != nil {
 			fmt.Fprintf(os.Stderr, "Error reading input: %v\n", err)
 			os.Exit(1)

cmd/bd/validate.go

@@ -400,17 +400,21 @@ func validateGitConflicts(_ context.Context, fix bool) checkResult {
 	if len(conflictLines) > 0 {
 		result.issueCount = 1 // One conflict situation
 		result.suggestions = append(result.suggestions,
-			fmt.Sprintf("Resolve git conflict in %s (markers at lines: %v)", jsonlPath, conflictLines))
+			fmt.Sprintf("Git conflict markers found in %s at lines: %v", jsonlPath, conflictLines))
-		if !fix {
+		result.suggestions = append(result.suggestions,
-			result.suggestions = append(result.suggestions,
+			"To resolve, choose one version:")
-				fmt.Sprintf("Then run 'bd import -i %s' to reload issues", jsonlPath))
+		result.suggestions = append(result.suggestions,
-		}
+			"  git checkout --ours .beads/issues.jsonl && bd import -i .beads/issues.jsonl")
+		result.suggestions = append(result.suggestions,
+			"  git checkout --theirs .beads/issues.jsonl && bd import -i .beads/issues.jsonl")
+		result.suggestions = append(result.suggestions,
+			"For advanced field-level merging: https://github.com/neongreen/mono/tree/main/beads-merge")
 	}
 
 	// Can't auto-fix git conflicts
 	if fix && result.issueCount > 0 {
 		result.suggestions = append(result.suggestions,
-			"Git conflicts cannot be auto-fixed. Resolve manually in your editor or run 'bd export' to regenerate JSONL")
+			"Note: Git conflicts cannot be auto-fixed with --fix-all")
 	}
 
 	return result