refactor(doctor): consolidate maintenance commands + improve daemon startup
Consolidate clean, repair-deps, validate into bd doctor: - Add validation checks to doctor (merge artifacts, orphaned deps, duplicates, test pollution, git conflicts) - Add auto-fix for merge artifacts and orphaned dependencies - Delete obsolete command files: clean.go, repair_deps.go, validate.go - Delete orphaned test files: clean_security_test.go, validate_test.go Improve daemon startup performance: - Add fast-fail detection when daemon crashed (check lock before retrying) - Reduce graceful shutdown timeout from 5s to 1s - Skip daemon connection for root command (just shows help) - Extract shutdown timeout as constants (daemonShutdownTimeout, daemonShutdownPollInterval) Other changes: - Move rename-prefix command to Maintenance group in help - Fix Makefile to inject git commit hash via ldflags New files: - cmd/bd/doctor/validation.go (5 check functions) - cmd/bd/doctor/fix/validation.go (2 fix functions)
This commit is contained in:
Ryan Snodgrass
committed by
Steve Yegge
Steve Yegge
parent
e60dfaf1f1
commit
cafc0b9dfb
168
cmd/bd/doctor/fix/validation.go
Normal file
168
cmd/bd/doctor/fix/validation.go
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@@ -0,0 +1,168 @@
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package fix
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import (
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"bufio"
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"database/sql"
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"fmt"
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"os"
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"path/filepath"
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"strings"
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_ "github.com/ncruces/go-sqlite3/driver"
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_ "github.com/ncruces/go-sqlite3/embed"
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)
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// MergeArtifacts removes temporary git merge files from .beads directory.
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func MergeArtifacts(path string) error {
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if err := validateBeadsWorkspace(path); err != nil {
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return err
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}
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beadsDir := filepath.Join(path, ".beads")
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// Read patterns from .gitignore or use defaults
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patterns, err := readMergeArtifactPatterns(beadsDir)
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if err != nil {
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patterns = []string{
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"*.base.jsonl",
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"*.left.jsonl",
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"*.right.jsonl",
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"*.meta.json",
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}
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}
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// Find and delete matching files
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var deleted int
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var errors []string
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for _, pattern := range patterns {
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matches, err := filepath.Glob(filepath.Join(beadsDir, pattern))
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if err != nil {
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continue
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}
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for _, file := range matches {
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if err := os.Remove(file); err != nil {
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if !os.IsNotExist(err) {
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errors = append(errors, fmt.Sprintf("%s: %v", filepath.Base(file), err))
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}
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} else {
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deleted++
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fmt.Printf(" Removed %s\n", filepath.Base(file))
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}
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}
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}
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if len(errors) > 0 {
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return fmt.Errorf("failed to remove some files: %s", strings.Join(errors, "; "))
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}
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if deleted == 0 {
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fmt.Println(" No merge artifacts to remove")
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} else {
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fmt.Printf(" Removed %d merge artifact(s)\n", deleted)
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}
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return nil
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}
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// readMergeArtifactPatterns reads patterns from .beads/.gitignore merge section
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func readMergeArtifactPatterns(beadsDir string) ([]string, error) {
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gitignorePath := filepath.Join(beadsDir, ".gitignore")
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file, err := os.Open(gitignorePath) // #nosec G304 - path constructed from beadsDir
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if err != nil {
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return nil, err
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}
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defer file.Close()
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var patterns []string
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inMergeSection := false
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scanner := bufio.NewScanner(file)
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for scanner.Scan() {
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line := strings.TrimSpace(scanner.Text())
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if strings.Contains(line, "Merge artifacts") {
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inMergeSection = true
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continue
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}
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if inMergeSection && strings.HasPrefix(line, "#") {
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break
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}
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if inMergeSection && line != "" && !strings.HasPrefix(line, "#") && !strings.HasPrefix(line, "!") {
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patterns = append(patterns, line)
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}
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}
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return patterns, scanner.Err()
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}
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// OrphanedDependencies removes dependencies pointing to non-existent issues.
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func OrphanedDependencies(path string) error {
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if err := validateBeadsWorkspace(path); err != nil {
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return err
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}
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beadsDir := filepath.Join(path, ".beads")
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dbPath := filepath.Join(beadsDir, "beads.db")
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// Open database
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db, err := openDB(dbPath)
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if err != nil {
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return fmt.Errorf("failed to open database: %w", err)
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}
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defer db.Close()
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// Find orphaned dependencies
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query := `
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SELECT d.issue_id, d.depends_on_id
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FROM dependencies d
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LEFT JOIN issues i ON d.depends_on_id = i.id
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WHERE i.id IS NULL
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`
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rows, err := db.Query(query)
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if err != nil {
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return fmt.Errorf("failed to query orphaned dependencies: %w", err)
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}
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defer rows.Close()
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type orphan struct {
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issueID string
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dependsOnID string
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}
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var orphans []orphan
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for rows.Next() {
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var o orphan
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if err := rows.Scan(&o.issueID, &o.dependsOnID); err == nil {
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orphans = append(orphans, o)
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}
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}
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if len(orphans) == 0 {
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fmt.Println(" No orphaned dependencies to fix")
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return nil
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}
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// Delete orphaned dependencies
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for _, o := range orphans {
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_, err := db.Exec("DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
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o.issueID, o.dependsOnID)
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if err != nil {
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fmt.Printf(" Warning: failed to remove %s→%s: %v\n", o.issueID, o.dependsOnID, err)
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} else {
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// Mark issue as dirty for export
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_, _ = db.Exec("INSERT OR IGNORE INTO dirty_issues (issue_id) VALUES (?)", o.issueID)
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fmt.Printf(" Removed orphaned dependency: %s→%s\n", o.issueID, o.dependsOnID)
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}
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}
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fmt.Printf(" Fixed %d orphaned dependency reference(s)\n", len(orphans))
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return nil
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}
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// openDB opens a SQLite database for read-write access
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func openDB(dbPath string) (*sql.DB, error) {
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return sql.Open("sqlite3", dbPath)
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}
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358
cmd/bd/doctor/validation.go
Normal file
358
cmd/bd/doctor/validation.go
Normal file
@@ -0,0 +1,358 @@
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package doctor
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import (
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"bufio"
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"bytes"
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"fmt"
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"os"
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"path/filepath"
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"strings"
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"github.com/steveyegge/beads/internal/beads"
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"github.com/steveyegge/beads/internal/storage/sqlite"
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"github.com/steveyegge/beads/internal/types"
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)
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// CheckMergeArtifacts detects temporary git merge files in .beads directory.
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// These are created during git merges and should be cleaned up.
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func CheckMergeArtifacts(path string) DoctorCheck {
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beadsDir := filepath.Join(path, ".beads")
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if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
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return DoctorCheck{
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Name: "Merge Artifacts",
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Status: "ok",
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Message: "N/A (no .beads directory)",
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}
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}
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// Read patterns from .beads/.gitignore (merge artifacts section)
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patterns, err := readMergeArtifactPatterns(beadsDir)
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if err != nil {
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// No .gitignore or can't read it - use default patterns
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patterns = []string{
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"*.base.jsonl",
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"*.left.jsonl",
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"*.right.jsonl",
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"*.meta.json",
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}
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}
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// Find matching files
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var artifacts []string
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for _, pattern := range patterns {
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matches, err := filepath.Glob(filepath.Join(beadsDir, pattern))
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if err != nil {
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continue
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}
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artifacts = append(artifacts, matches...)
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}
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if len(artifacts) == 0 {
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return DoctorCheck{
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Name: "Merge Artifacts",
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Status: "ok",
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Message: "No merge artifacts found",
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}
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}
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// Build list of relative paths for display
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var relPaths []string
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for _, f := range artifacts {
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if rel, err := filepath.Rel(beadsDir, f); err == nil {
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relPaths = append(relPaths, rel)
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}
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}
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return DoctorCheck{
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Name: "Merge Artifacts",
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Status: "warning",
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Message: fmt.Sprintf("%d temporary merge file(s) found", len(artifacts)),
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Detail: strings.Join(relPaths, ", "),
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Fix: "Run 'bd doctor --fix' to remove merge artifacts",
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}
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}
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// readMergeArtifactPatterns reads patterns from .beads/.gitignore merge section
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func readMergeArtifactPatterns(beadsDir string) ([]string, error) {
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gitignorePath := filepath.Join(beadsDir, ".gitignore")
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file, err := os.Open(gitignorePath) // #nosec G304 - path constructed from beadsDir
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if err != nil {
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return nil, err
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}
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defer file.Close()
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var patterns []string
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inMergeSection := false
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scanner := bufio.NewScanner(file)
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for scanner.Scan() {
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line := strings.TrimSpace(scanner.Text())
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if strings.Contains(line, "Merge artifacts") {
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inMergeSection = true
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continue
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}
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if inMergeSection && strings.HasPrefix(line, "#") {
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break
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}
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if inMergeSection && line != "" && !strings.HasPrefix(line, "#") && !strings.HasPrefix(line, "!") {
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patterns = append(patterns, line)
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}
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}
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return patterns, scanner.Err()
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}
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// CheckOrphanedDependencies detects dependencies pointing to non-existent issues.
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func CheckOrphanedDependencies(path string) DoctorCheck {
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beadsDir := filepath.Join(path, ".beads")
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dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
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if _, err := os.Stat(dbPath); os.IsNotExist(err) {
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return DoctorCheck{
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Name: "Orphaned Dependencies",
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Status: "ok",
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Message: "N/A (no database)",
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}
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}
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// Open database read-only
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db, err := openDBReadOnly(dbPath)
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if err != nil {
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return DoctorCheck{
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Name: "Orphaned Dependencies",
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Status: "ok",
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Message: "N/A (unable to open database)",
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}
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}
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defer db.Close()
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// Query for orphaned dependencies
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query := `
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SELECT d.issue_id, d.depends_on_id, d.type
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FROM dependencies d
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LEFT JOIN issues i ON d.depends_on_id = i.id
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WHERE i.id IS NULL
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`
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rows, err := db.Query(query)
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if err != nil {
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return DoctorCheck{
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Name: "Orphaned Dependencies",
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Status: "ok",
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Message: "N/A (query failed)",
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}
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}
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defer rows.Close()
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var orphans []string
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for rows.Next() {
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var issueID, dependsOnID, depType string
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if err := rows.Scan(&issueID, &dependsOnID, &depType); err == nil {
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orphans = append(orphans, fmt.Sprintf("%s→%s", issueID, dependsOnID))
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}
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}
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if len(orphans) == 0 {
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return DoctorCheck{
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Name: "Orphaned Dependencies",
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Status: "ok",
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Message: "No orphaned dependencies",
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}
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}
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detail := strings.Join(orphans, ", ")
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if len(detail) > 200 {
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detail = detail[:200] + "..."
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}
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return DoctorCheck{
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Name: "Orphaned Dependencies",
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Status: "warning",
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Message: fmt.Sprintf("%d orphaned dependency reference(s)", len(orphans)),
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Detail: detail,
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Fix: "Run 'bd doctor --fix' to remove orphaned dependencies",
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}
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}
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// CheckDuplicateIssues detects issues with identical content.
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func CheckDuplicateIssues(path string) DoctorCheck {
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beadsDir := filepath.Join(path, ".beads")
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dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
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if _, err := os.Stat(dbPath); os.IsNotExist(err) {
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return DoctorCheck{
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Name: "Duplicate Issues",
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Status: "ok",
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Message: "N/A (no database)",
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}
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}
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// Open store to use existing duplicate detection
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store, err := sqlite.New(nil, dbPath)
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if err != nil {
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return DoctorCheck{
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Name: "Duplicate Issues",
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Status: "ok",
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Message: "N/A (unable to open database)",
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}
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}
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defer func() { _ = store.Close() }()
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issues, err := store.SearchIssues(nil, "", types.IssueFilter{})
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if err != nil {
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return DoctorCheck{
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Name: "Duplicate Issues",
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Status: "ok",
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Message: "N/A (unable to query issues)",
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}
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}
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// Find duplicates by title+description hash
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seen := make(map[string][]string) // hash -> list of IDs
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for _, issue := range issues {
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if issue.Status == types.StatusTombstone {
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continue
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}
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key := issue.Title + "|" + issue.Description
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seen[key] = append(seen[key], issue.ID)
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}
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var duplicateGroups int
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var totalDuplicates int
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for _, ids := range seen {
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if len(ids) > 1 {
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duplicateGroups++
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totalDuplicates += len(ids) - 1 // exclude the canonical one
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}
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}
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|
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if duplicateGroups == 0 {
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return DoctorCheck{
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Name: "Duplicate Issues",
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Status: "ok",
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Message: "No duplicate issues",
|
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}
|
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}
|
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|
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return DoctorCheck{
|
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Name: "Duplicate Issues",
|
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Status: "warning",
|
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Message: fmt.Sprintf("%d duplicate issue(s) in %d group(s)", totalDuplicates, duplicateGroups),
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Detail: "Duplicates cannot be auto-fixed",
|
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Fix: "Run 'bd duplicates' to review and merge duplicates",
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}
|
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}
|
||||
|
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// CheckTestPollution detects test issues that may have leaked into the database.
|
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func CheckTestPollution(path string) DoctorCheck {
|
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beadsDir := filepath.Join(path, ".beads")
|
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dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
|
||||
|
||||
if _, err := os.Stat(dbPath); os.IsNotExist(err) {
|
||||
return DoctorCheck{
|
||||
Name: "Test Pollution",
|
||||
Status: "ok",
|
||||
Message: "N/A (no database)",
|
||||
}
|
||||
}
|
||||
|
||||
db, err := openDBReadOnly(dbPath)
|
||||
if err != nil {
|
||||
return DoctorCheck{
|
||||
Name: "Test Pollution",
|
||||
Status: "ok",
|
||||
Message: "N/A (unable to open database)",
|
||||
}
|
||||
}
|
||||
defer db.Close()
|
||||
|
||||
// Look for common test patterns in titles
|
||||
query := `
|
||||
SELECT COUNT(*) FROM issues
|
||||
WHERE status != 'tombstone'
|
||||
AND (
|
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title LIKE 'test-%' OR
|
||||
title LIKE 'Test Issue%' OR
|
||||
title LIKE '%test issue%' OR
|
||||
id LIKE 'test-%'
|
||||
)
|
||||
`
|
||||
var count int
|
||||
if err := db.QueryRow(query).Scan(&count); err != nil {
|
||||
return DoctorCheck{
|
||||
Name: "Test Pollution",
|
||||
Status: "ok",
|
||||
Message: "N/A (query failed)",
|
||||
}
|
||||
}
|
||||
|
||||
if count == 0 {
|
||||
return DoctorCheck{
|
||||
Name: "Test Pollution",
|
||||
Status: "ok",
|
||||
Message: "No test pollution detected",
|
||||
}
|
||||
}
|
||||
|
||||
return DoctorCheck{
|
||||
Name: "Test Pollution",
|
||||
Status: "warning",
|
||||
Message: fmt.Sprintf("%d potential test issue(s) detected", count),
|
||||
Detail: "Test issues may have leaked into production database",
|
||||
Fix: "Run 'bd detect-pollution' to review and clean test issues",
|
||||
}
|
||||
}
|
||||
|
||||
// CheckGitConflicts detects git conflict markers in JSONL file.
|
||||
func CheckGitConflicts(path string) DoctorCheck {
|
||||
beadsDir := filepath.Join(path, ".beads")
|
||||
jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
|
||||
|
||||
if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
|
||||
return DoctorCheck{
|
||||
Name: "Git Conflicts",
|
||||
Status: "ok",
|
||||
Message: "N/A (no JSONL file)",
|
||||
}
|
||||
}
|
||||
|
||||
data, err := os.ReadFile(jsonlPath) // #nosec G304 - path constructed safely
|
||||
if err != nil {
|
||||
return DoctorCheck{
|
||||
Name: "Git Conflicts",
|
||||
Status: "ok",
|
||||
Message: "N/A (unable to read JSONL)",
|
||||
}
|
||||
}
|
||||
|
||||
// Look for conflict markers at start of lines
|
||||
lines := bytes.Split(data, []byte("\n"))
|
||||
var conflictLines []int
|
||||
for i, line := range lines {
|
||||
trimmed := bytes.TrimSpace(line)
|
||||
if bytes.HasPrefix(trimmed, []byte("<<<<<<< ")) ||
|
||||
bytes.Equal(trimmed, []byte("=======")) ||
|
||||
bytes.HasPrefix(trimmed, []byte(">>>>>>> ")) {
|
||||
conflictLines = append(conflictLines, i+1)
|
||||
}
|
||||
}
|
||||
|
||||
if len(conflictLines) == 0 {
|
||||
return DoctorCheck{
|
||||
Name: "Git Conflicts",
|
||||
Status: "ok",
|
||||
Message: "No git conflicts in JSONL",
|
||||
}
|
||||
}
|
||||
|
||||
return DoctorCheck{
|
||||
Name: "Git Conflicts",
|
||||
Status: "error",
|
||||
Message: fmt.Sprintf("Git conflict markers found at %d location(s)", len(conflictLines)),
|
||||
Detail: fmt.Sprintf("Conflict markers at lines: %v", conflictLines),
|
||||
Fix: "Resolve conflicts manually: git checkout --ours or --theirs .beads/issues.jsonl",
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user