fix: sync must not prune registry entries for installed skills

Sync's registry prune logic removed entries for installed skills whose
files were missing from disk. This was wrong: the registry is the
authoritative record of installations managed by install/uninstall.

Remove PruneStaleSkills calls from sync (CLI global, CLI project, and
web UI handler). Reconcile (called during install) still uses prune
with full metadata context, which is correct.

Fixes: running 'sync' after 'install' would clear registry.yaml when
the installed skill's source files were not yet on disk.

Author: runkids

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.18.8] - 2026-04-06
+
+### Bug Fixes
+
+- **Sync no longer deletes registry entries for installed skills** — running `skillshare sync` (or project-mode `sync -p`) would silently remove `registry.yaml` entries for skills whose source files were not present on disk. This meant that installing a skill and then syncing could erase the installation record entirely. Sync now leaves the registry untouched — only `install` and `uninstall` manage registry entries
+
 ## [0.18.7] - 2026-04-04
 
 ### New Features

cmd/skillshare/sync.go

@@ -240,33 +240,9 @@ func cmdSync(args []string) error {
 		}
 	}
 
-	// Prune stale registry entries using already-discovered skills (avoids second walk)
-	if !dryRun {
-		regDir := cfg.RegistryDir
-		if regDir == "" {
-			regDir = config.SourceRoot(cfg.Source)
-		}
-		reg, regErr := config.LoadRegistry(regDir)
-		if regErr == nil {
-			live := make(map[string]bool, len(discoveredSkills))
-			for _, s := range discoveredSkills {
-				live[s.RelPath] = true
-			}
-			// Ignored skills still exist on disk — don't prune their registry entries
-			if ignoreStats != nil {
-				for _, p := range ignoreStats.IgnoredSkills {
-					live[p] = true
-				}
-			}
-			var pruneChanged bool
-			reg.Skills, pruneChanged = config.PruneStaleSkills(reg.Skills, live, false)
-			if pruneChanged {
-				if err := reg.Save(regDir); err != nil {
-					fmt.Fprintf(os.Stderr, "warning: failed to save registry after prune: %v\n", err)
-				}
-			}
-		}
-	}
+	// Registry entries are managed by install/uninstall, not sync.
+	// Sync only manages symlinks — it must not prune registry entries
+	// for installed skills whose files may be missing from disk.
 
 	logSyncOp(config.ConfigPath(), syncLogStats{
 		Targets: len(cfg.Targets),

cmd/skillshare/sync_project.go

@@ -3,7 +3,6 @@ package main
 import (
 	"fmt"
 	"os"
-	"path/filepath"
 	"time"
 
 	"skillshare/internal/config"
@@ -136,24 +135,9 @@ func cmdSyncProject(root string, dryRun, force, jsonOutput bool) (syncLogStats,
 			}
 		}
 
-		// Prune stale registry entries using already-discovered skills (avoids second walk)
-		live := make(map[string]bool, len(discoveredSkills))
-		for _, s := range discoveredSkills {
-			live[s.RelPath] = true
-		}
-		// Ignored skills still exist on disk — don't prune their registry entries
-		if ignoreStats != nil {
-			for _, p := range ignoreStats.IgnoredSkills {
-				live[p] = true
-			}
-		}
-		var pruneChanged bool
-		runtime.registry.Skills, pruneChanged = config.PruneStaleSkills(runtime.registry.Skills, live, true)
-		if pruneChanged {
-			if err := runtime.registry.Save(filepath.Join(root, ".skillshare")); err != nil {
-				fmt.Fprintf(os.Stderr, "warning: failed to save registry after prune: %v\n", err)
-			}
-		}
+		// Registry entries are managed by install/uninstall, not sync.
+		// Sync only manages symlinks — it must not prune registry entries
+		// for installed skills whose files may be missing from disk.
 	}
 
 	if failedTargets > 0 {

internal/server/handler_sync.go

@@ -2,10 +2,8 @@ package server
 
 import (
 	"encoding/json"
-	"log"
 	"maps"
 	"net/http"
-	"path/filepath"
 	"time"
 
 	"skillshare/internal/config"
@@ -80,34 +78,9 @@ func (s *Server) handleSync(w http.ResponseWriter, r *http.Request) {
 		warnings = append(warnings, "source directory is empty (0 skills)")
 	}
 
-	// Prune stale registry entries using already-discovered skills (avoids second walk).
-	// Uses defer so early returns from target errors still trigger cleanup.
-	if !body.DryRun {
-		defer func() {
-			live := make(map[string]bool, len(allSkills))
-			for _, sk := range allSkills {
-				live[sk.RelPath] = true
-			}
-			// Ignored skills still exist on disk — don't prune their registry entries
-			if ignoreStats != nil {
-				for _, p := range ignoreStats.IgnoredSkills {
-					live[p] = true
-				}
-			}
-			skillsOnly := s.IsProjectMode() // project registries also store agent entries
-			var pruneChanged bool
-			s.registry.Skills, pruneChanged = config.PruneStaleSkills(s.registry.Skills, live, skillsOnly)
-			if pruneChanged {
-				regDir := s.cfg.RegistryDir
-				if s.IsProjectMode() {
-					regDir = filepath.Join(s.projectRoot, ".skillshare")
-				}
-				if err := s.registry.Save(regDir); err != nil {
-					log.Printf("warning: failed to save registry after prune: %v", err)
-				}
-			}
-		}()
-	}
+	// Registry entries are managed by install/uninstall, not sync.
+	// Sync only manages symlinks — it must not prune registry entries
+	// for installed skills whose files may be missing from disk.
 
 	results := make([]syncTargetResult, 0)
 

tests/integration/sync_project_test.go

@@ -5,6 +5,7 @@ package integration
 import (
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"skillshare/internal/testutil"
@@ -110,6 +111,39 @@ func TestSyncProject_DryRun_NoChanges(t *testing.T) {
 	}
 }
 
+func TestSyncProject_PreservesRegistryEntries(t *testing.T) {
+	sb := testutil.NewSandbox(t)
+	defer sb.Cleanup()
+	projectRoot := sb.SetupProjectDir("claude")
+
+	// Create a skill on disk that sync will discover
+	sb.CreateProjectSkill(projectRoot, "local-skill", map[string]string{
+		"SKILL.md": "# Local Skill",
+	})
+
+	// Write a registry with a remote-installed skill that has NO files on disk.
+	// Sync must NOT prune this entry — the registry is the source of truth for installations.
+	registryPath := filepath.Join(projectRoot, ".skillshare", "registry.yaml")
+	registryContent := "skills:\n  - name: remote-tool\n    source: github.com/someone/remote-tool\n"
+	os.WriteFile(registryPath, []byte(registryContent), 0644)
+
+	result := sb.RunCLIInDir(projectRoot, "sync", "-p")
+	result.AssertSuccess(t)
+
+	// Verify registry still contains the remote-tool entry
+	data, err := os.ReadFile(registryPath)
+	if err != nil {
+		t.Fatalf("failed to read registry: %v", err)
+	}
+	content := string(data)
+	if !strings.Contains(content, "remote-tool") {
+		t.Errorf("sync should preserve registry entry for installed skill without local files, got:\n%s", content)
+	}
+	if !strings.Contains(content, "github.com/someone/remote-tool") {
+		t.Errorf("sync should preserve source in registry entry, got:\n%s", content)
+	}
+}
+
 func TestSyncProject_AutoDetectsMode(t *testing.T) {
 	sb := testutil.NewSandbox(t)
 	defer sb.Cleanup()

tests/integration/sync_test.go

@@ -6,6 +6,7 @@ import (
 	"encoding/json"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"skillshare/internal/testutil"
@@ -464,6 +465,41 @@ targets:
 	}
 }
 
+func TestSync_PreservesRegistryEntries(t *testing.T) {
+	sb := testutil.NewSandbox(t)
+	defer sb.Cleanup()
+
+	// Create a local skill that sync will discover
+	sb.CreateSkill("local-skill", map[string]string{"SKILL.md": "# Local"})
+
+	targetPath := sb.CreateTarget("claude")
+	sb.WriteConfig(`source: ` + sb.SourcePath + `
+mode: merge
+targets:
+  claude:
+    path: ` + targetPath + `
+`)
+
+	// Write a registry with a remote-installed skill that has NO files on disk.
+	// Sync must NOT prune this entry — registry is the source of truth for installations.
+	registryPath := filepath.Join(sb.SourcePath, "registry.yaml")
+	registryContent := "skills:\n  - name: remote-tool\n    source: github.com/someone/remote-tool\n"
+	os.WriteFile(registryPath, []byte(registryContent), 0644)
+
+	result := sb.RunCLI("sync")
+	result.AssertSuccess(t)
+
+	// Verify registry still contains the remote-tool entry
+	data, err := os.ReadFile(registryPath)
+	if err != nil {
+		t.Fatalf("failed to read registry: %v", err)
+	}
+	content := string(data)
+	if !strings.Contains(content, "remote-tool") {
+		t.Errorf("sync should preserve registry entry for installed skill without local files, got:\n%s", content)
+	}
+}
+
 func TestSync_MergeMode_IncludeFilter(t *testing.T) {
 	sb := testutil.NewSandbox(t)
 	defer sb.Cleanup()

website/src/pages/changelog.md

@@ -9,6 +9,12 @@ All notable changes to skillshare are documented here. For the full commit histo
 
 ---
 
+## [0.18.8] - 2026-04-06
+
+### Bug Fixes
+
+- **Sync no longer deletes registry entries for installed skills** — running `skillshare sync` (or project-mode `sync -p`) would silently remove `registry.yaml` entries for skills whose source files were not present on disk. This meant that installing a skill and then syncing could erase the installation record entirely. Sync now leaves the registry untouched — only `install` and `uninstall` manage registry entries
+
 ## [0.18.7] - 2026-04-04
 
 ### New Features