fix: CI test failures and lint errors

- Fixed test file naming: issues.jsonl -> beads.jsonl
  - beads_test.go: Update expected path in TestFindJSONLPath
  - internal/beads/beads_test.go: Update TestFindJSONLPathDefault
  - cmd/bd/main_test.go: Update TestAutoFlushJSONLContent

- Fixed lint errors (gosec):
  - G304: Added nosec comments for file operations with user-provided paths
  - G204: Added nosec comment for subprocess with controlled binary path

- Fixed lint errors (errcheck):
  - cmd/bd/test_wait_helper.go: Acknowledge error return values with _
  - cmd/bd/onboard.go: Handle fmt.Fprintf error return

All tests passing locally. All lint checks passing.

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

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

cmd/bd/doctor/fix/sync_branch.go

@@ -32,6 +32,7 @@ func SyncBranchConfig(path string) error {
 	}
 
 	// Set sync.branch using bd config set
+	// #nosec G204 - bdBinary is controlled by getBdBinary() which returns os.Executable()
 	setCmd := exec.Command(bdBinary, "config", "set", "sync.branch", currentBranch)
 	setCmd.Dir = path
 	if output, err := setCmd.CombinedOutput(); err != nil {