bd-o2e: Add --squash flag to bd sync for batching commits

For solo developers who don't need real-time multi-agent coordination,
--squash accumulates changes in JSONL without committing. Run 'bd sync'
later (without --squash) to commit all accumulated changes in one commit.

This reduces git history noise while preserving the default behavior
needed for multi-agent orchestration.

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

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

cmd/bd/doctor.go

@@ -2258,11 +2258,7 @@ func checkUntrackedBeadsFiles(path string) doctorCheck {
 	}
 }
 
-// countIssuesInJSONLFile counts the number of issues in a JSONL file
-func countIssuesInJSONLFile(jsonlPath string) int {
-	count, _, _ := countJSONLIssues(jsonlPath)
-	return count
-}
+// NOTE: countIssuesInJSONLFile is defined in init.go
 
 // detectPrefixFromJSONL detects the most common issue prefix from a JSONL file
 func detectPrefixFromJSONL(jsonlPath string) string {