fix(ci): more changes to fix failing CI (#415)

Fixes from maphew including:
- Remove test for deleted isPathWithinDir function
- Add gosec nolint directives for safe file operations
- Add rm -rf .beads before init in CI workflow
- Simplify panic handling and file operations

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

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

cmd/bd/doctor.go

@@ -661,6 +661,7 @@ func checkDatabaseVersion(path string) doctorCheck {
 			// Check config.yaml for no-db: true
 			configPath := filepath.Join(beadsDir, "config.yaml")
 			isNoDbMode := false
+			// #nosec G304 -- configPath is constructed from beadsDir which is in .beads/
 			if configData, err := os.ReadFile(configPath); err == nil {
 				// Simple check for no-db: true in config.yaml
 				isNoDbMode = strings.Contains(string(configData), "no-db: true")
@@ -1513,6 +1514,13 @@ func countJSONLIssues(jsonlPath string) (int, map[string]int, error) {
 	return count, prefixes, nil
 }
 
+// countIssuesInJSONLFile counts the number of valid issues in a JSONL file.
+// This is a wrapper around countJSONLIssues that returns only the count.
+func countIssuesInJSONLFile(jsonlPath string) int {
+	count, _, _ := countJSONLIssues(jsonlPath)
+	return count
+}
+
 func checkPermissions(path string) doctorCheck {
 	beadsDir := filepath.Join(path, ".beads")