feat: add archive_prefix for core-specific BIOS subdirectories

Closes #43

FBNeo and Kronos expect BIOS archives in core-specific subdirectories
(system/fbneo/, system/kronos/). RetroArch firmware check uses .info
paths which include these prefixes, so files at root show as Missing.

Add archive_prefix field to emulator profiles. The pack code now places
archive copies in the prefixed subdirectory while keeping root copies
for cores that expect them there (e.g. Geolith for neogeo.zip).

scripts/generate_pack.py

@@ -337,6 +337,8 @@ def _collect_emulator_extras(
     from common import resolve_platform_cores
     from verify import find_undeclared_files
 
+    profiles = emu_profiles if emu_profiles is not None else load_emulator_profiles(emulators_dir)
+
     undeclared = find_undeclared_files(config, emulators_dir, db, emu_profiles, target_cores=target_cores)
     extras = []
     seen_dests: set[str] = set(seen)
@@ -364,7 +366,6 @@ def _collect_emulator_extras(
     # different path by another core (e.g. neocd/ vs root, same_cdi/bios/ vs root).
     # Only adds a copy when the file is ALREADY covered at a different path -
     # never introduces a file that wasn't selected by the first pass.
-    profiles = emu_profiles if emu_profiles is not None else load_emulator_profiles(emulators_dir)
     relevant = resolve_platform_cores(config, profiles, target_cores=target_cores)
     standalone_set = {str(c) for c in config.get("standalone_cores", [])}
     by_name = db.get("indexes", {}).get("by_name", {})
@@ -422,6 +423,41 @@ def _collect_emulator_extras(
                 "source_emulator": profile.get("emulator", emu_name),
             })
 
+    # Archive prefix pass: cores that store BIOS archives in a subdirectory
+    # (e.g. system/fbneo/neogeo.zip).  When the archive is already covered at
+    # the root, add a copy at the prefixed path so the core's .info firmware
+    # check finds it.
+    for emu_name, profile in sorted(profiles.items()):
+        if profile.get("type") in ("launcher", "alias"):
+            continue
+        if emu_name not in relevant:
+            continue
+        prefix = profile.get("archive_prefix", "")
+        if not prefix:
+            continue
+        profile_archives: set[str] = set()
+        for f in profile.get("files", []):
+            archive = f.get("archive", "")
+            if archive:
+                profile_archives.add(archive)
+        for archive_name in sorted(profile_archives):
+            if archive_name not in covered_names:
+                continue
+            dest = f"{prefix}/{archive_name}"
+            full_dest = f"{base_dest}/{dest}" if base_dest else dest
+            if full_dest in seen_dests:
+                continue
+            if not by_name.get(archive_name):
+                continue
+            seen_dests.add(full_dest)
+            extras.append({
+                "name": archive_name,
+                "destination": dest,
+                "required": True,
+                "hle_fallback": False,
+                "source_emulator": profile.get("emulator", emu_name),
+            })
+
     # Third pass: agnostic scan — for filename-agnostic cores, include all
     # DB files matching the system path prefix and size criteria.
     files_db = db.get("files", {})
@@ -1066,9 +1102,10 @@ def generate_pack(
             if _has_path_conflict(full_dest, seen_destinations, seen_parents):
                 continue
 
+            dest_hint = fe.get("destination", "")
             local_path, status = resolve_file(
                 fe, db, bios_dir, zip_contents,
-                data_dir_registry=data_registry,
+                dest_hint=dest_hint, data_dir_registry=data_registry,
             )
             if status in ("not_found", "external", "user_provided"):
                 continue
@@ -1181,6 +1218,9 @@ def _normalize_zip_for_pack(source_zip: str, dest_path: str, target_zf: zipfile.
     try:
         rebuild_zip_deterministic(source_zip, tmp_path)
         target_zf.write(tmp_path, dest_path)
+    except zipfile.BadZipFile:
+        # Corrupt source ZIP: copy as-is (will be flagged by verify)
+        target_zf.write(source_zip, dest_path)
     finally:
         os.unlink(tmp_path)
 
@@ -1318,8 +1358,11 @@ def generate_emulator_pack(
                     archives.add(archive)
 
             # Pack archives as units
+            archive_prefix = profile.get("archive_prefix", "")
             for archive_name in sorted(archives):
                 archive_dest = _sanitize_path(archive_name)
+                if archive_prefix:
+                    archive_dest = f"{archive_prefix}/{archive_dest}"
                 if pack_structure:
                     mode_key = "standalone" if standalone else "libretro"
                     prefix = pack_structure.get(mode_key, "")
@@ -2262,7 +2305,9 @@ def generate_manifest(
         if _has_path_conflict(full_dest, seen_destinations, seen_parents):
             continue
 
-        local_path, status = resolve_file(fe, db, bios_dir, zip_contents)
+        dest_hint = fe.get("destination", "")
+        local_path, status = resolve_file(fe, db, bios_dir, zip_contents,
+                                          dest_hint=dest_hint)
         if status in ("not_found", "external", "user_provided"):
             continue