feat(sync): prevent zombie resurrection from stale clones
Add JSONL sanitization after git pull to remove deleted issues that git's 3-way merge may resurrect. Also add bd doctor check to hydrate deletions.jsonl from git history for pre-v0.25.0 deletions. Changes: - Add sanitizeJSONLWithDeletions() in sync.go (Step 3.6) - Add checkDeletionsManifest() in doctor.go (Check 18) - Add HydrateDeletionsManifest() fix in doctor/fix/deletions.go - Add looksLikeIssueID() validation to prevent false positives - Add comprehensive tests for sanitization logic 🤖 Generated with Claude Code Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
Steve Yegge
223
cmd/bd/doctor/fix/deletions.go
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223
cmd/bd/doctor/fix/deletions.go
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package fix
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import (
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"bufio"
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"encoding/json"
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"fmt"
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"os"
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"os/exec"
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"path/filepath"
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"strings"
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"time"
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"github.com/steveyegge/beads/internal/deletions"
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)
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// HydrateDeletionsManifest populates deletions.jsonl from git history.
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// It finds all issue IDs that were ever in the JSONL but are no longer present,
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// and adds them to the deletions manifest.
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func HydrateDeletionsManifest(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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jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
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// Also check for legacy issues.jsonl
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if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
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legacyPath := filepath.Join(beadsDir, "issues.jsonl")
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if _, err := os.Stat(legacyPath); err == nil {
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jsonlPath = legacyPath
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} else {
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return fmt.Errorf("no JSONL file found in .beads/")
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}
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}
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// Load existing deletions manifest to avoid duplicates
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deletionsPath := deletions.DefaultPath(beadsDir)
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existingDeletions, err := deletions.LoadDeletions(deletionsPath)
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if err != nil {
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return fmt.Errorf("failed to load existing deletions: %w", err)
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}
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// Get current IDs from JSONL
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currentIDs, err := getCurrentJSONLIDs(jsonlPath)
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if err != nil {
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return fmt.Errorf("failed to read current JSONL: %w", err)
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}
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// Get historical IDs from git
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historicalIDs, err := getHistoricalJSONLIDs(path, jsonlPath)
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if err != nil {
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return fmt.Errorf("failed to get historical IDs from git: %w", err)
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}
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// Find deleted IDs (in history but not in current, and not already in manifest)
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var deletedIDs []string
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for id := range historicalIDs {
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if !currentIDs[id] {
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// Skip if already in deletions manifest
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if _, exists := existingDeletions.Records[id]; exists {
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continue
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}
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deletedIDs = append(deletedIDs, id)
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}
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}
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if len(deletedIDs) == 0 {
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fmt.Println(" No new deleted issues found in git history")
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return nil
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}
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// Add to deletions manifest
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now := time.Now()
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for _, id := range deletedIDs {
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record := deletions.DeletionRecord{
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ID: id,
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Timestamp: now,
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Actor: "bd-doctor-hydrate",
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Reason: "Hydrated from git history",
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}
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if err := deletions.AppendDeletion(deletionsPath, record); err != nil {
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return fmt.Errorf("failed to append deletion record for %s: %w", id, err)
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}
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}
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fmt.Printf(" Added %d deletion records to manifest\n", len(deletedIDs))
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return nil
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}
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// getCurrentJSONLIDs reads the current JSONL file and returns a set of IDs.
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func getCurrentJSONLIDs(jsonlPath string) (map[string]bool, error) {
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ids := make(map[string]bool)
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file, err := os.Open(jsonlPath) // #nosec G304 - path validated by caller
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if err != nil {
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if os.IsNotExist(err) {
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return ids, nil
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}
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return nil, err
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}
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defer file.Close()
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scanner := bufio.NewScanner(file)
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scanner.Buffer(make([]byte, 0, 64*1024), 10*1024*1024)
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for scanner.Scan() {
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line := scanner.Bytes()
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if len(line) == 0 {
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continue
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}
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var issue struct {
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ID string `json:"id"`
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}
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if err := json.Unmarshal(line, &issue); err != nil {
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continue
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}
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if issue.ID != "" {
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ids[issue.ID] = true
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}
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}
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return ids, scanner.Err()
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}
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// getHistoricalJSONLIDs uses git log to find all IDs that were ever in the JSONL.
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func getHistoricalJSONLIDs(repoPath, jsonlPath string) (map[string]bool, error) {
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// Get the relative path for the JSONL file
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relPath, err := filepath.Rel(repoPath, jsonlPath)
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if err != nil {
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relPath = jsonlPath
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}
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// Use the commit-by-commit approach which is more memory efficient
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// and allows us to properly parse JSON rather than regex matching
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return getHistoricalIDsViaDiff(repoPath, relPath)
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}
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// looksLikeIssueID validates that a string looks like a beads issue ID.
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// Issue IDs have the format: prefix-hash or prefix-number (e.g., bd-abc123, myproject-42)
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func looksLikeIssueID(id string) bool {
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if id == "" {
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return false
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}
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// Must contain at least one dash
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dashIdx := strings.Index(id, "-")
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if dashIdx <= 0 || dashIdx >= len(id)-1 {
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return false
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}
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// Prefix should be alphanumeric (letters/numbers/underscores)
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prefix := id[:dashIdx]
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for _, c := range prefix {
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if !((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z') || (c >= '0' && c <= '9') || c == '_') {
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return false
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}
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}
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// Suffix should be alphanumeric (base36 hash or number), may contain dots for children
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suffix := id[dashIdx+1:]
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for _, c := range suffix {
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if !((c >= 'a' && c <= 'z') || (c >= '0' && c <= '9') || c == '.') {
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return false
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}
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}
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return true
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}
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// getHistoricalIDsViaDiff walks through git history commit-by-commit to find all IDs.
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// This is more memory efficient than git log -p and allows proper JSON parsing.
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func getHistoricalIDsViaDiff(repoPath, relPath string) (map[string]bool, error) {
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ids := make(map[string]bool)
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// Get list of all commits that touched the file
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cmd := exec.Command("git", "log", "--all", "--format=%H", "--", relPath)
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cmd.Dir = repoPath
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output, err := cmd.Output()
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if err != nil {
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return ids, fmt.Errorf("git log failed: %w", err)
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}
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commits := strings.Split(strings.TrimSpace(string(output)), "\n")
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if len(commits) == 0 || (len(commits) == 1 && commits[0] == "") {
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return ids, nil
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}
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// For each commit, get the file content and extract IDs
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for _, commit := range commits {
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if commit == "" {
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continue
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}
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// Get file content at this commit
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showCmd := exec.Command("git", "show", commit+":"+relPath)
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showCmd.Dir = repoPath
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content, err := showCmd.Output()
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if err != nil {
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// File might not exist at this commit
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continue
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}
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// Parse each line for IDs
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scanner := bufio.NewScanner(strings.NewReader(string(content)))
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for scanner.Scan() {
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line := scanner.Text()
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if strings.Contains(line, `"id"`) {
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var issue struct {
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ID string `json:"id"`
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}
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if err := json.Unmarshal([]byte(line), &issue); err == nil && issue.ID != "" {
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// Validate the ID looks like an issue ID to avoid false positives
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if looksLikeIssueID(issue.ID) {
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ids[issue.ID] = true
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}
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}
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}
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}
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}
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return ids, nil
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}
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