Fix db recover when repo.RefList is nil

It tries to find dangling references but repo has no reference list and
it ended up with a nice trace
```
root@hostname:/usr/scratch/agustin/aptly-stress-tester# aptly db recover
Recovering database...
Checking database integrity...
panic: runtime error: invalid memory address or nil pointer dereference [recovered]
        panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x13b9c24]

goroutine 1 [running]:
github.com/aptly-dev/aptly/cmd.Run.func1()
        /home/tin/projects/aptly/cmd/run.go:17 +0xc5
panic({0x15abf60?, 0x2da1650?})
        /usr/local/go/src/runtime/panic.go:792 +0x132
github.com/aptly-dev/aptly/deb.(*PackageRefList).ForEach(...)
        /home/tin/projects/aptly/deb/reflist.go:83
github.com/aptly-dev/aptly/deb.FindDanglingReferences(...)
        /home/tin/projects/aptly/deb/find_dangling.go:15
github.com/aptly-dev/aptly/cmd.checkRepo(0xc0015827e0)
        /home/tin/projects/aptly/cmd/db_recover.go:63 +0xa4
github.com/aptly-dev/aptly/cmd.checkIntegrity.(*LocalRepoCollection).ForEach.func1({0xc0002fc2d0?, 0xc0010c2018?, 0x1?}, {0xc11004c000, 0xb9, 0xe0})
        /home/tin/projects/aptly/deb/local.go:229 +0xa7
github.com/aptly-dev/aptly/database/goleveldb.(*storage).ProcessByPrefix(0xc0005ae140?, {0xc0010c2018, 0x1, 0x1}, 0xc00107be40)
        /home/tin/projects/aptly/database/goleveldb/storage.go:114 +0x184
github.com/aptly-dev/aptly/deb.(*LocalRepoCollection).ForEach(...)
        /home/tin/projects/aptly/deb/local.go:222
github.com/aptly-dev/aptly/cmd.checkIntegrity()
        /home/tin/projects/aptly/cmd/db_recover.go:51 +0x7f
github.com/aptly-dev/aptly/cmd.aptlyDBRecover(0x40ed4e?, {0xc0003b5c30?, 0x2?, 0xc00057bdb0?})
        /home/tin/projects/aptly/cmd/db_recover.go:27 +0x93
github.com/smira/commander.(*Command).Dispatch(0xc00052c900, {0xc0003b5c30, 0x0, 0x0})
        /go/pkg/mod/github.com/smira/commander@v0.0.0-20140515201010-f408b00e68d5/commands.go:305 +0xd1
github.com/smira/commander.(*Command).Dispatch(0xc00052ca20, {0xc0003b5c30, 0x1, 0x1})
        /go/pkg/mod/github.com/smira/commander@v0.0.0-20140515201010-f408b00e68d5/commands.go:283 +0x165
github.com/smira/commander.(*Command).Dispatch(0xc000516000, {0xc0003b5c20, 0x2, 0x2})
        /go/pkg/mod/github.com/smira/commander@v0.0.0-20140515201010-f408b00e68d5/commands.go:283 +0x165
github.com/aptly-dev/aptly/cmd.Run(0xc000516000, {0xc000194280?, 0x0?, 0x24a5bc8?}, 0x1)
        /home/tin/projects/aptly/cmd/run.go:41 +0x1b9
main.main()
        /home/tin/projects/aptly/main.go:27 +0x10d
```

After applying the fix you get
```
root@hostname:~/aptly-stress-tester# aptly db recover
Recovering database...
Checking database integrity...
Warning: Repo "stress_test_repo_3532" has no reference list (severely corrupted), initializing empty list
Warning: Repo "stress_test_repo_9244" has no reference list (severely corrupted), initializing empty list
```

Also it tries better to avoid nil references in repos, and snapshots

Author: agustinhenze

cmd/db_recover.go

@@ -57,20 +57,37 @@ func checkRepo(repo *deb.LocalRepo) error {
 
 	err := repos.LoadComplete(repo)
 	if err != nil {
-		return fmt.Errorf("load complete repo %q: %s", repo.Name, err)
+		// If we can't load the repo, it might be severely corrupted
+		// Log the error but continue with other repos
+		context.Progress().Printf("Warning: Cannot load repo %q: %s\n", repo.Name, err)
+		return nil
 	}
 
-	dangling, err := deb.FindDanglingReferences(repo.RefList(), collectionFactory.PackageCollection())
+	// Check if RefList is nil (severe corruption case)
+	refList := repo.RefList()
+	if refList == nil {
+		context.Progress().Printf("Warning: Repo %q has no reference list (severely corrupted), initializing empty list\n", repo.Name)
+		// Initialize with empty reflist
+		repo.UpdateRefList(deb.NewPackageRefList())
+		if err = repos.Update(repo); err != nil {
+			return fmt.Errorf("update repo with empty reflist: %w", err)
+		}
+		return nil
+	}
+
+	dangling, err := deb.FindDanglingReferences(refList, collectionFactory.PackageCollection())
 	if err != nil {
-		return fmt.Errorf("find dangling references: %w", err)
+		// If we can't find dangling references, log but continue
+		context.Progress().Printf("Warning: Cannot check dangling references for repo %q: %s\n", repo.Name, err)
+		return nil
 	}
 
-	if len(dangling.Refs) > 0 {
+	if dangling != nil && len(dangling.Refs) > 0 {
 		for _, ref := range dangling.Refs {
 			context.Progress().Printf("Removing dangling database reference %q\n", ref)
 		}
 
-		repo.UpdateRefList(repo.RefList().Subtract(dangling))
+		repo.UpdateRefList(refList.Subtract(dangling))
 
 		if err = repos.Update(repo); err != nil {
 			return fmt.Errorf("update repo: %w", err)

deb/local.go

@@ -160,9 +160,15 @@ func (collection *LocalRepoCollection) Add(repo *LocalRepo) error {
 func (collection *LocalRepoCollection) Update(repo *LocalRepo) error {
 	batch := collection.db.CreateBatch()
 	_ = batch.Put(repo.Key(), repo.Encode())
+
 	if repo.packageRefs != nil {
 		_ = batch.Put(repo.RefKey(), repo.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(repo.RefKey())
 	}
+
 	return batch.Write()
 }
 

deb/remote.go

@@ -847,11 +847,16 @@ func (collection *RemoteRepoCollection) Add(repo *RemoteRepo) error {
 // Update stores updated information about repo in DB
 func (collection *RemoteRepoCollection) Update(repo *RemoteRepo) error {
 	batch := collection.db.CreateBatch()
-
 	_ = batch.Put(repo.Key(), repo.Encode())
+
 	if repo.packageRefs != nil {
 		_ = batch.Put(repo.RefKey(), repo.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(repo.RefKey())
 	}
+
 	return batch.Write()
 }
 

deb/snapshot.go

@@ -227,10 +227,14 @@ func (collection *SnapshotCollection) Add(snapshot *Snapshot) error {
 // Update stores updated information about snapshot in DB
 func (collection *SnapshotCollection) Update(snapshot *Snapshot) error {
 	batch := collection.db.CreateBatch()
-
 	_ = batch.Put(snapshot.Key(), snapshot.Encode())
+
 	if snapshot.packageRefs != nil {
 		_ = batch.Put(snapshot.RefKey(), snapshot.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(snapshot.RefKey())
 	}
 
 	return batch.Write()