fix(skills): fix dep detection false positives and all-or-nothing install

- Filter Python stdlib modules at scan time to prevent false positives
  when the runtime checker fails (e.g. pip:argparse, pip:sys)
- Install pip/npm packages one-by-one instead of batch so partial
  success is preserved when one package fails
- Persist missing deps to DB after install via StoreMissingDeps() so
  reload reflects actual state instead of stale data
- Use explicit master tenant context in handleInstallDeps for
  consistency with rescanAndUpdate()

internal/http/skills.go

@@ -255,7 +255,11 @@ func (h *SkillsHandler) handleInstallDeps(w http.ResponseWriter, r *http.Request
 	if !h.requireMasterTenant(w, r) {
 		return
 	}
-	dirs := h.skills.ListSystemSkillDirs(r.Context())
+	// Use explicit master tenant context for system skill operations,
+	// consistent with rescanAndUpdate() pattern.
+	masterCtx := store.WithTenantID(r.Context(), store.MasterTenantID)
+
+	dirs := h.skills.ListSystemSkillDirs(masterCtx)
 	if len(dirs) == 0 {
 		writeJSON(w, http.StatusOK, map[string]string{"message": "no system skills"})
 		return
@@ -274,25 +278,24 @@ func (h *SkillsHandler) handleInstallDeps(w http.ResponseWriter, r *http.Request
 		})
 	}
 
-	result, err := installManagedDeps(r.Context(), manifest, missing)
+	result, err := installManagedDeps(masterCtx, manifest, missing)
 	if err != nil {
 		writeJSON(w, http.StatusInternalServerError, map[string]string{"error": err.Error()})
 		return
 	}
 
-	// Re-check all system skills and update status after install
-	allSkills := h.skills.ListAllSkills(r.Context())
+	// Re-check all system skills, persist missing deps, and update status.
+	allSkills := h.skills.ListAllSkills(masterCtx)
+	statusChanged := false
 	for _, sk := range allSkills {
 		if !sk.IsSystem {
 			continue
 		}
-		dir, exists := dirs[sk.Slug]
-		if !exists {
+		if _, exists := dirs[sk.Slug]; !exists {
 			continue
 		}
 		m := h.scanWithFallback(sk)
 		if m == nil || m.IsEmpty() {
-			_ = dir // dir was used for direct scan; fallback uses sk.BaseDir
 			continue
 		}
 		ok, miss := skills.CheckSkillDeps(m)
@@ -300,10 +303,20 @@ func (h *SkillsHandler) handleInstallDeps(w http.ResponseWriter, r *http.Request
 		if err != nil {
 			continue
 		}
-		if ok && sk.Status == "archived" {
-			_ = h.skills.UpdateSkill(r.Context(), id, map[string]any{"status": "active"})
-			h.skills.BumpVersion()
+
+		// Persist actual missing deps to DB so reload reflects reality.
+		_ = h.skills.StoreMissingDeps(masterCtx, id, miss)
+
+		// Update status in both directions.
+		switch {
+		case ok && sk.Status == "archived":
+			_ = h.skills.UpdateSkill(masterCtx, id, map[string]any{"status": "active"})
+			statusChanged = true
+		case !ok && sk.Status != "archived":
+			_ = h.skills.UpdateSkill(masterCtx, id, map[string]any{"status": "archived"})
+			statusChanged = true
 		}
+
 		status := "active"
 		if !ok {
 			status = "archived"
@@ -319,6 +332,9 @@ func (h *SkillsHandler) handleInstallDeps(w http.ResponseWriter, r *http.Request
 			})
 		}
 	}
+	if statusChanged {
+		h.skills.BumpVersion()
+	}
 
 	if h.msgBus != nil {
 		h.msgBus.Broadcast(bus.Event{