diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index 506cc677..00e00f77 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -190,9 +190,16 @@ except Exception:
                     local candidate="$presets_dir/$preset_id/templates/${template_name}.md"
                     [ -f "$candidate" ] && echo "$candidate" && return 0
                 done <<< "$sorted_presets"
+            else
+                # python3 returned empty list — fall through to directory scan
+                for preset in "$presets_dir"/*/; do
+                    [ -d "$preset" ] || continue
+                    local candidate="$preset/templates/${template_name}.md"
+                    [ -f "$candidate" ] && echo "$candidate" && return 0
+                done
             fi
         else
-            # Fallback: alphabetical directory order
+            # Fallback: alphabetical directory order (no python3 available)
             for preset in "$presets_dir"/*/; do
                 [ -d "$preset" ] || continue
                 local candidate="$preset/templates/${template_name}.md"
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index 47fb69de..63d6dd63 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -189,7 +189,7 @@ function Resolve-Template {
     # Priority 3: Extension-provided templates
     $extDir = Join-Path $RepoRoot '.specify/extensions'
     if (Test-Path $extDir) {
-        foreach ($ext in Get-ChildItem -Path $extDir -Directory -ErrorAction SilentlyContinue) {
+        foreach ($ext in Get-ChildItem -Path $extDir -Directory -ErrorAction SilentlyContinue | Where-Object { $_.Name -notlike '.*' } | Sort-Object Name) {
             $candidate = Join-Path $ext.FullName "templates/$TemplateName.md"
             if (Test-Path $candidate) { return $candidate }
         }
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 593e2e7a..a7746fd0 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1574,6 +1574,19 @@ def init(
             else:
                 tracker.skip("git", "--no-git flag")
 
+            # Persist the CLI options so later operations (e.g. preset add)
+            # can adapt their behaviour without re-scanning the filesystem.
+            # Must be saved BEFORE preset install so _get_skills_dir() works.
+            save_init_options(project_path, {
+                "ai": selected_ai,
+                "ai_skills": ai_skills,
+                "ai_commands_dir": ai_commands_dir,
+                "here": here,
+                "preset": preset,
+                "script": selected_script,
+                "speckit_version": get_speckit_version(),
+            })
+
             # Install preset if specified
             if preset:
                 try:
@@ -1590,23 +1603,16 @@ def init(
                         try:
                             zip_path = preset_catalog.download_pack(preset)
                             preset_manager.install_from_zip(zip_path, speckit_ver)
+                            # Clean up downloaded ZIP to avoid cache accumulation
+                            try:
+                                zip_path.unlink(missing_ok=True)
+                            except Exception:
+                                pass
                         except PresetError:
                             console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
                 except Exception as preset_err:
                     console.print(f"[yellow]Warning:[/yellow] Failed to install preset: {preset_err}")
 
-            # Persist the CLI options so later operations (e.g. preset add)
-            # can adapt their behaviour without re-scanning the filesystem.
-            save_init_options(project_path, {
-                "ai": selected_ai,
-                "ai_skills": ai_skills,
-                "ai_commands_dir": ai_commands_dir,
-                "here": here,
-                "preset": preset,
-                "script": selected_script,
-                "speckit_version": get_speckit_version(),
-            })
-
             tracker.complete("final", "project ready")
         except Exception as e:
             tracker.error("final", str(e))
@@ -1957,6 +1963,14 @@ def preset_add(
             console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")
 
         elif from_url:
+            # Validate URL scheme before downloading
+            from urllib.parse import urlparse as _urlparse
+            _parsed = _urlparse(from_url)
+            _is_localhost = _parsed.hostname in ("localhost", "127.0.0.1", "::1")
+            if _parsed.scheme != "https" and not (_parsed.scheme == "http" and _is_localhost):
+                console.print(f"[red]Error:[/red] URL must use HTTPS (got {_parsed.scheme}://). HTTP is only allowed for localhost.")
+                raise typer.Exit(1)
+
             console.print(f"Installing preset from [cyan]{from_url}[/cyan]...")
             import urllib.request
             import urllib.error
diff --git a/src/specify_cli/extensions.py b/src/specify_cli/extensions.py
index 03cb3afa..9053db50 100644
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -522,7 +522,7 @@ class ExtensionManager:
         # Unregister commands from all AI agents
         if registered_commands:
             registrar = CommandRegistrar()
-            registrar._registrar.unregister_commands(registered_commands, self.project_root)
+            registrar.unregister_commands(registered_commands, self.project_root)
 
         if keep_config:
             # Preserve config files, only remove non-config files
@@ -714,6 +714,14 @@ class CommandRegistrar:
             context_note=context_note
         )
 
+    def unregister_commands(
+        self,
+        registered_commands: Dict[str, List[str]],
+        project_root: Path
+    ) -> None:
+        """Remove previously registered command files from agent directories."""
+        self._registrar.unregister_commands(registered_commands, project_root)
+
     def register_commands_for_claude(
         self,
         manifest: ExtensionManifest,
diff --git a/src/specify_cli/presets.py b/src/specify_cli/presets.py
index 522fc4b5..5140865b 100644
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -1137,14 +1137,16 @@ class PresetCatalog:
         Raises:
             PresetError: If catalog cannot be fetched
         """
+        catalog_url = self.get_catalog_url()
+
         if not force_refresh and self.is_cache_valid():
             try:
-                return json.loads(self.cache_file.read_text())
-            except json.JSONDecodeError:
+                metadata = json.loads(self.cache_metadata_file.read_text())
+                if metadata.get("catalog_url") == catalog_url:
+                    return json.loads(self.cache_file.read_text())
+            except (json.JSONDecodeError, OSError):
                 pass
 
-        catalog_url = self.get_catalog_url()
-
         try:
             import urllib.request
             import urllib.error
@@ -1186,6 +1188,9 @@ class PresetCatalog:
     ) -> List[Dict[str, Any]]:
         """Search catalog for presets.
 
+        Searches across all active catalogs (merged by priority) so that
+        community and custom catalogs are included in results.
+
         Args:
             query: Search query (searches name, description, tags)
             tag: Filter by specific tag
@@ -1195,12 +1200,11 @@ class PresetCatalog:
             List of matching preset metadata
         """
         try:
-            catalog_data = self.fetch_catalog()
+            packs = self._get_merged_packs()
         except PresetError:
             return []
 
         results = []
-        packs = catalog_data.get("presets", {})
 
         for pack_id, pack_data in packs.items():
             if author and pack_data.get("author", "").lower() != author.lower():
@@ -1234,6 +1238,8 @@ class PresetCatalog:
     ) -> Optional[Dict[str, Any]]:
         """Get detailed information about a specific preset.
 
+        Searches across all active catalogs (merged by priority).
+
         Args:
             pack_id: ID of the preset
 
@@ -1241,11 +1247,10 @@ class PresetCatalog:
             Pack metadata or None if not found
         """
         try:
-            catalog_data = self.fetch_catalog()
+            packs = self._get_merged_packs()
         except PresetError:
             return None
 
-        packs = catalog_data.get("presets", {})
         if pack_id in packs:
             return {**packs[pack_id], "id": pack_id}
         return None
@@ -1369,16 +1374,18 @@ class PresetResolver:
         else:
             subdirs = [""]
 
+        # Determine file extension based on template type
+        ext = ".md"
+        if template_type == "script":
+            ext = ".sh"  # scripts use .sh; callers can also check .ps1
+
         # Priority 1: Project-local overrides
-        for subdir in subdirs:
-            if template_type == "script":
-                override = self.overrides_dir / "scripts" / f"{template_name}.sh"
-            elif subdir:
-                override = self.overrides_dir / f"{template_name}.md"
-            else:
-                override = self.overrides_dir / f"{template_name}.md"
-            if override.exists():
-                return override
+        if template_type == "script":
+            override = self.overrides_dir / "scripts" / f"{template_name}{ext}"
+        else:
+            override = self.overrides_dir / f"{template_name}{ext}"
+        if override.exists():
+            return override
 
         # Priority 2: Installed presets (sorted by priority — lower number wins)
         if self.presets_dir.exists():
@@ -1387,11 +1394,9 @@ class PresetResolver:
                 pack_dir = self.presets_dir / pack_id
                 for subdir in subdirs:
                     if subdir:
-                        candidate = (
-                            pack_dir / subdir / f"{template_name}.md"
-                        )
+                        candidate = pack_dir / subdir / f"{template_name}{ext}"
                     else:
-                        candidate = pack_dir / f"{template_name}.md"
+                        candidate = pack_dir / f"{template_name}{ext}"
                     if candidate.exists():
                         return candidate
 
@@ -1402,13 +1407,9 @@ class PresetResolver:
                     continue
                 for subdir in subdirs:
                     if subdir:
-                        candidate = (
-                            ext_dir / "templates" / f"{template_name}.md"
-                        )
+                        candidate = ext_dir / subdir / f"{template_name}{ext}"
                     else:
-                        candidate = (
-                            ext_dir / "templates" / f"{template_name}.md"
-                        )
+                        candidate = ext_dir / "templates" / f"{template_name}{ext}"
                     if candidate.exists():
                         return candidate
 
@@ -1421,6 +1422,10 @@ class PresetResolver:
             core = self.templates_dir / "commands" / f"{template_name}.md"
             if core.exists():
                 return core
+        elif template_type == "script":
+            core = self.templates_dir / "scripts" / f"{template_name}{ext}"
+            if core.exists():
+                return core
 
         return None
 
@@ -1438,52 +1443,34 @@ class PresetResolver:
         Returns:
             Dictionary with 'path' and 'source' keys, or None if not found
         """
-        # Priority 1: Project-local overrides
-        override = self.overrides_dir / f"{template_name}.md"
-        if override.exists():
-            return {"path": str(override), "source": "project override"}
+        # Delegate to resolve() for the actual lookup, then determine source
+        resolved = self.resolve(template_name, template_type)
+        if resolved is None:
+            return None
 
-        # Priority 2: Installed presets (sorted by priority — lower number wins)
-        if self.presets_dir.exists():
+        resolved_str = str(resolved)
+
+        # Determine source attribution
+        if str(self.overrides_dir) in resolved_str:
+            return {"path": resolved_str, "source": "project override"}
+
+        if str(self.presets_dir) in resolved_str and self.presets_dir.exists():
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
-                pack_dir = self.presets_dir / pack_id
-                # Check templates/ subdirectory first, then root
-                for subdir in ["templates", "commands", "scripts", ""]:
-                    if subdir:
-                        candidate = (
-                            pack_dir / subdir / f"{template_name}.md"
-                        )
-                    else:
-                        candidate = pack_dir / f"{template_name}.md"
-                    if candidate.exists():
-                        meta = registry.get(pack_id)
-                        version = meta.get("version", "?") if meta else "?"
-                        return {
-                            "path": str(candidate),
-                            "source": f"{pack_id} v{version}",
-                        }
-
-        # Priority 3: Extension-provided templates
-        if self.extensions_dir.exists():
-            for ext_dir in sorted(self.extensions_dir.iterdir()):
-                if not ext_dir.is_dir() or ext_dir.name.startswith("."):
-                    continue
-                candidate = ext_dir / "templates" / f"{template_name}.md"
-                if candidate.exists():
+                if f"/{pack_id}/" in resolved_str:
+                    meta = registry.get(pack_id)
+                    version = meta.get("version", "?") if meta else "?"
                     return {
-                        "path": str(candidate),
+                        "path": resolved_str,
+                        "source": f"{pack_id} v{version}",
+                    }
+
+        if str(self.extensions_dir) in resolved_str and self.extensions_dir.exists():
+            for ext_dir in sorted(self.extensions_dir.iterdir()):
+                if ext_dir.is_dir() and f"/{ext_dir.name}/" in resolved_str:
+                    return {
+                        "path": resolved_str,
                         "source": f"extension:{ext_dir.name}",
                     }
 
-        # Priority 4: Core templates
-        core = self.templates_dir / f"{template_name}.md"
-        if core.exists():
-            return {"path": str(core), "source": "core"}
-
-        # Also check commands subdirectory for core
-        core_cmd = self.templates_dir / "commands" / f"{template_name}.md"
-        if core_cmd.exists():
-            return {"path": str(core_cmd), "source": "core"}
-
-        return None
+        return {"path": resolved_str, "source": "core"}