diff --git a/manifestv2_app_ynh/convert_to_packaging_format_v2.py b/manifestv2_app_ynh/convert_to_packaging_format_v2.py
deleted file mode 100644
index 4e7b2f1..0000000
--- a/manifestv2_app_ynh/convert_to_packaging_format_v2.py
+++ /dev/null
@@ -1,146 +0,0 @@
-import copy
-import json
-
-
-def _convert_v1_manifest_to_v2(manifest):
-
-    manifest = copy.deepcopy(manifest)
-
-    if "upstream" not in manifest:
-        manifest["upstream"] = {}
-
-    if "license" in manifest and "license" not in manifest["upstream"]:
-        manifest["upstream"]["license"] = manifest["license"]
-
-    if "url" in manifest and "website" not in manifest["upstream"]:
-        manifest["upstream"]["website"] = manifest["url"]
-
-    manifest["integration"] = {
-        "yunohost": manifest.get("requirements", {}).get("yunohost"),
-        "architectures": "all",
-        "multi_instance": manifest.get("multi_instance", False),
-        "ldap": "?",
-        "sso": "?",
-    }
-
-    maintainer = manifest.get("maintainer", {}).get("name")
-    manifest["maintainers"] = [maintainer] if maintainer else []
-
-    install_questions = manifest["arguments"]["install"]
-    manifest["install"] = {}
-    for question in install_questions:
-        name = question.pop("name")
-        if "ask" in question and name in ["domain", "path", "admin", "is_public", "password"]:
-            question.pop("ask")
-        if question.get("example") and question.get("type") in ["domain", "path", "user", "boolean", "password"]:
-            question.pop("example")
-
-        manifest["install"][name] = question
-
-    manifest["resources"] = {
-        "disk": {
-            "build": "50M",     # This is an *estimate* minimum value for the disk needed at build time (e.g. during install/upgrade) and during regular usage
-            "usage": "50M"      # Please only use round values such as: 10M, 100M, 200M, 400M, 800M, 1G, 2G, 4G, 8G
-        },
-        "ram": {
-            "build": "50M",     # This is an *estimate* minimum value for the RAM needed at build time (i.e. during install/upgrade) and during regular usage
-            "usage": "10M",     # Please only use round values like ["10M", "100M", "200M", "400M", "800M", "1G", "2G", "4G", "8G"]
-            "include_swap": False
-        },
-        "route": {},
-        "install_dir": {
-            "base_dir": "/var/www/",  # This means that the app shall be installed in /var/www/$app which is the standard for webapps. You may change this to /opt/ if the app is a system app.
-            "alias": "final_path"
-        }
-    }
-
-    if "domain" in manifest["install"] and "path" in manifest["install"]:
-        manifest["resources"]["route"]["url"] = "{domain}{path}"
-    elif "path" not in manifest["install"]:
-        manifest["resources"]["route"]["url"] = "{domain}/"
-    else:
-        del manifest["resources"]["route"]
-
-    keys_to_keep = ["packaging_format", "id", "name", "description", "version", "maintainers", "upstream", "integration", "install", "resources"]
-
-    keys_to_del = [key for key in manifest.keys() if key not in keys_to_keep]
-    for key in keys_to_del:
-        del manifest[key]
-
-    return manifest
-
-
-def _dump_v2_manifest_as_toml(manifest):
-
-    import re
-    from tomlkit import document, nl, table, dumps, comment
-
-    toml_manifest = document()
-    toml_manifest.add("packaging_format", 2)
-    toml_manifest.add(nl())
-    toml_manifest.add("id", manifest["id"])
-    toml_manifest.add("name", manifest["name"])
-    for lang, value in manifest["description"].items():
-        toml_manifest.add(f"description.{lang}", value)
-    toml_manifest.add(nl())
-    toml_manifest.add("version", manifest["version"])
-    toml_manifest.add(nl())
-    toml_manifest.add("maintainers", manifest["maintainers"])
-
-    upstream = table()
-    for key, value in manifest["upstream"].items():
-        upstream[key] = value
-    toml_manifest["upstream"] = upstream
-
-    integration = table()
-    for key, value in manifest["integration"].items():
-        integration[key] = value
-    integration["architectures"].comment('Can be replaced by a list of supported archs using the dpkg --print-architecture nomenclature, for example: ["amd64", "i386"]')
-    toml_manifest["integration"] = integration
-
-    install = table()
-    for key, value in manifest["install"].items():
-        install[key] = table()
-        install[key].indent(4)
-
-        if key in ["domain", "path", "admin", "is_public", "password"]:
-            install[key].add(comment("this is a generic question - ask strings are automatically handled by Yunohost's core"))
-
-        for lang, value2 in value.get("ask", {}).items():
-            install[key].add(f"ask.{lang}", value2)
-
-        for lang, value2 in value.get("help", {}).items():
-            install[key].add(f"help.{lang}", value2)
-
-        for key2, value2 in value.items():
-            if key2 in ["ask", "help"]:
-                continue
-            install[key].add(key2, value2)
-
-    toml_manifest["install"] = install
-
-    resources = table()
-    for key, value in manifest["resources"].items():
-        resources[key] = table()
-        resources[key].indent(4)
-        for key2, value2 in value.items():
-            resources[key].add(key2, value2)
-            if key in ["disk", "ram"] and key2 == "build":
-                resources[key][key2].comment(f"This is an *estimate* minimum value for the {key} needed at build time (e.g. during install/upgrade) and during regular usage")
-            elif key in ["disk", "ram"] and key2 == "usage":
-                resources[key][key2].comment("Please only use round values such as: 10M, 100M, 200M, 400M, 800M, 1G, 2G, 4G, 8G")
-            elif key == "install_dir" and key2 == "base_dir":
-                resources[key][key2].comment("This means that the app shall be installed in /var/www/$app which is the standard for webapps. You may change this to /opt/ if the app is a system app.")
-
-    toml_manifest["resources"] = resources
-
-    toml_manifest_dump = dumps(toml_manifest)
-
-    regex = re.compile(r'\"((description|ask|help)\.[a-z]{2})\"')
-    toml_manifest_dump = regex.sub(r'\1', toml_manifest_dump)
-    return toml_manifest_dump
-
-
-manifest = json.load(open("manifest.json"))
-manifest = _convert_v1_manifest_to_v2(manifest)
-print(_dump_v2_manifest_as_toml(manifest))
diff --git a/manifestv2_app_ynh/convert_to_packaging_v2.py b/manifestv2_app_ynh/convert_to_packaging_v2.py
new file mode 100644
index 0000000..5603955
--- /dev/null
+++ b/manifestv2_app_ynh/convert_to_packaging_v2.py
@@ -0,0 +1,310 @@
+import os
+import re
+import json
+import subprocess
+
+
+def check_output(cmd):
+    return (
+        subprocess.check_output(cmd, shell=True)
+        .decode("utf-8")
+        .strip()
+    )
+
+
+def _convert_v1_manifest_to_v2(app_path):
+
+    manifest = json.load(open(app_path + "/manifest.json"))
+
+    if "upstream" not in manifest:
+        manifest["upstream"] = {}
+
+    if "license" in manifest and "license" not in manifest["upstream"]:
+        manifest["upstream"]["license"] = manifest["license"]
+
+    if "url" in manifest and "website" not in manifest["upstream"]:
+        manifest["upstream"]["website"] = manifest["url"]
+
+    manifest["integration"] = {
+        "yunohost": manifest.get("requirements", {}).get("yunohost"),
+        "architectures": "all",
+        "multi_instance": manifest.get("multi_instance", False),
+        "ldap": "?",
+        "sso": "?",
+        "disk": "50M",
+        "ram.build": "50M",
+        "ram.runtime": "50M"
+    }
+
+    maintainer = manifest.get("maintainer", {}).get("name")
+    manifest["maintainers"] = [maintainer] if maintainer else []
+
+    install_questions = manifest["arguments"]["install"]
+    manifest["install"] = {}
+    for question in install_questions:
+        name = question.pop("name")
+        if "ask" in question and name in ["domain", "path", "admin", "is_public", "password"]:
+            question.pop("ask")
+        if question.get("example") and question.get("type") in ["domain", "path", "user", "boolean", "password"]:
+            question.pop("example")
+
+        manifest["install"][name] = question
+
+    # Rename is_public to init_main_permission
+    manifest["install"] = {(k if k != "is_public" else "init_main_permission"): v for k, v in manifest["install"].items()}
+
+    if "init_main_permission" in manifest["install"]:
+        manifest["install"]["init_main_permission"]["type"] = "group"
+        if manifest["install"]["init_main_permission"].get("default") is True:
+            manifest["install"]["init_main_permission"]["default"] = "visitors"
+        elif manifest["install"]["init_main_permission"].get("default") is True:
+            manifest["install"]["init_main_permission"]["default"] = "all_users"
+
+    if "domain" in manifest["install"] and "path" not in manifest["install"]:
+        manifest["install"]["domain"]["full_domain"] = True
+
+    manifest["resources"] = {}
+    manifest["resources"]["system_user"] = {}
+    manifest["resources"]["install_dir"] = {}
+
+    if os.system(f"grep -q 'datadir=' {app_path}/scripts/install") == 0:
+        manifest["resources"]["data_dir"] = {}
+
+    manifest["resources"]["permissions"] = {}
+
+    if os.system(f"grep -q 'ynh_webpath_register' '{app_path}/scripts/install'") == 0:
+        manifest["resources"]["permissions"]["main.url"] = "/"
+
+    # FIXME: Parse ynh_permission_create --permission="admin" --url="/wp-login.php" --additional_urls="/wp-admin.php" --allowed=$admin_wordpress
+
+    ports = check_output(f"sed -nr 's/(\\w+)=.*ynh_find_port[^0-9]*([0-9]+)\\)/\\1,\\2/p' '{app_path}/scripts/install'")
+    if ports:
+        manifest["resources"]["ports"] = {}
+        for port in ports.split("\n"):
+            name, default = port.split(",")
+            exposed = check_output(f"sed -nr 's/.*yunohost firewall allow .*(TCP|UDP|Both).*${name}/\\1/p' '{app_path}/scripts/install'")
+            if exposed == "Both":
+                exposed = True
+
+            name = name.replace("_port", "").replace("port_", "")
+            if name == "port":
+                name = "main"
+
+            manifest["resources"]["ports"][f"{name}.default"] = int(default)
+            if exposed:
+                manifest["resources"]["ports"][f"{name}.exposed"] = exposed
+
+    maybequote = "[\"'\"'\"']?"
+    apt_dependencies = check_output(f"sed -nr 's/.*_dependencies={maybequote}(.*){maybequote}? *$/\\1/p' '{app_path}/scripts/_common.sh' | tr -d '\"' | sed 's@ @\\n@g'")
+    php_version = check_output(f"sed -nr 's/^ *YNH_PHP_VERSION={maybequote}(.*){maybequote}?$/\\1/p' '{app_path}/scripts/_common.sh' | tr -d \"\\\"'\"")
+    if apt_dependencies.strip():
+        if php_version:
+            apt_dependencies = apt_dependencies.replace("${YNH_PHP_VERSION}", php_version)
+        apt_dependencies = ', '.join([d for d in apt_dependencies.split("\n") if d])
+        manifest["resources"]["apt"] = {"packages": apt_dependencies}
+
+    extra_apt_repos = check_output(r"sed -nr 's/.*_extra_app_dependencies.*repo=\"(.*)\".*package=\"(.*)\".*key=\"(.*)\"/\1,\2,\3/p' %s/scripts/install" % app_path)
+    if extra_apt_repos:
+        for i, extra_apt_repo in enumerate(extra_apt_repos.split("\n")):
+            repo, packages, key = extra_apt_repo.split(",")
+            packages = packages.replace('$', '#FIXME#$')
+            if "apt" not in manifest["resources"]:
+                manifest["resources"]["apt"] = {}
+            if "extras" not in manifest["resources"]["apt"]:
+                manifest["resources"]["apt"]["extras"] = []
+            manifest["resources"]["apt"]["extras"].append({
+                "repo": repo,
+                "key": key,
+                "packages": packages,
+            })
+
+    if os.system(f"grep -q 'ynh_mysql_setup_db' {app_path}/scripts/install") == 0:
+        manifest["resources"]["database"] = {"type": "mysql"}
+    elif os.system(f"grep -q 'ynh_psql_setup_db' {app_path}/scripts/install") == 0:
+        manifest["resources"]["database"] = {"type": "postgresql"}
+
+    keys_to_keep = ["packaging_format", "id", "name", "description", "version", "maintainers", "upstream", "integration", "install", "resources"]
+
+    keys_to_del = [key for key in manifest.keys() if key not in keys_to_keep]
+    for key in keys_to_del:
+        del manifest[key]
+
+    return manifest
+
+
+def _dump_v2_manifest_as_toml(manifest):
+
+    import re
+    from tomlkit import document, nl, table, dumps, comment
+
+    toml_manifest = document()
+    toml_manifest.add("packaging_format", 2)
+    toml_manifest.add(nl())
+    toml_manifest.add("id", manifest["id"])
+    toml_manifest.add("name", manifest["name"])
+    for lang, value in manifest["description"].items():
+        toml_manifest.add(f"description.{lang}", value)
+    toml_manifest.add(nl())
+    toml_manifest.add("version", manifest["version"])
+    toml_manifest.add(nl())
+    toml_manifest.add("maintainers", manifest["maintainers"])
+
+    upstream = table()
+    for key, value in manifest["upstream"].items():
+        upstream[key] = value
+    toml_manifest["upstream"] = upstream
+
+    integration = table()
+    for key, value in manifest["integration"].items():
+        integration.add(key, value)
+    integration["architectures"].comment('FIXME: can be replaced by a list of supported archs using the dpkg --print-architecture nomenclature (amd64/i386/armhf/arm64/armel), for example: ["amd64", "i386"]')
+    integration["ldap"].comment('FIXME: replace with true, false, or "not_relevant"')
+    integration["sso"].comment('FIXME: replace with true, false, or "not_relevant"')
+    integration["disk"].comment('FIXME: replace with an **estimate** minimum disk requirement. e.g. 20M, 400M, 1G, ...')
+    integration["ram.build"].comment('FIXME: replace with an **estimate** minimum ram requirement. e.g. 50M, 400M, 1G, ...')
+    integration["ram.runtime"].comment('FIXME: replace with an **estimate** minimum ram requirement. e.g. 50M, 400M, 1G, ...')
+    toml_manifest["integration"] = integration
+
+    install = table()
+    for key, value in manifest["install"].items():
+        install[key] = table()
+        install[key].indent(4)
+
+        if key in ["domain", "path", "admin", "is_public", "password"]:
+            install[key].add(comment("this is a generic question - ask strings are automatically handled by Yunohost's core"))
+
+        for lang, value2 in value.get("ask", {}).items():
+            install[key].add(f"ask.{lang}", value2)
+
+        for lang, value2 in value.get("help", {}).items():
+            install[key].add(f"help.{lang}", value2)
+
+        for key2, value2 in value.items():
+            if key2 in ["ask", "help"]:
+                continue
+            install[key].add(key2, value2)
+
+    toml_manifest["install"] = install
+
+    resources = table()
+    for key, value in manifest["resources"].items():
+        resources[key] = table()
+        resources[key].indent(4)
+        for key2, value2 in value.items():
+            resources[key].add(key2, value2)
+            if key == "apt" and key2 == "extras":
+                for extra in resources[key][key2]:
+                    extra.indent(8)
+
+    toml_manifest["resources"] = resources
+
+    toml_manifest_dump = dumps(toml_manifest)
+
+    regex = re.compile(r'\"((description|ask|help)\.[a-z]{2})\"')
+    toml_manifest_dump = regex.sub(r'\1', toml_manifest_dump)
+    toml_manifest_dump = toml_manifest_dump.replace('"ram.build"', "ram.build")
+    toml_manifest_dump = toml_manifest_dump.replace('"ram.runtime"', "ram.runtime")
+    toml_manifest_dump = toml_manifest_dump.replace('"main.url"', "main.url")
+    toml_manifest_dump = toml_manifest_dump.replace('"main.default"', "main.default")
+    return toml_manifest_dump
+
+
+def cleanup_scripts_and_conf(folder):
+
+    patterns_to_remove_in_scripts = [
+        "^.*ynh_abort_if_errors.*$",
+        "^.*YNH_APP_ARG.*$",
+        "^.*YNH_APP_INSTANCE_NAME.*$",
+        r"^ *final_path=",
+        r"^\s*final_path=",
+        "^.*test .*-(e|d) .*final_path.*$",
+        "^.*ynh_webpath_register.*$",
+        "^.*ynh_webpath_available.*$",
+        "^.*ynh_system_user_create.*$",
+        "^.*ynh_system_user_delete.*$",
+        "^.*ynh_permission_update.*$",
+        "^.*ynh_permission_create.*$",
+        "^.*if .*ynh_permission_exists.*$",
+        "^.*if .*ynh_legacy_permissions_exists.*$",
+        "^.*ynh_legacy_permissions_delete_all.*$",
+        "^.*ynh_app_setting_set .*(domain|path|final_path|admin|password|port|datadir|db_name|db_user|db_pwd).*$",
+        "^.*ynh_app_setting_.* is_public.*$",
+        r"^.*if.*\$is_public.*$",
+        "^.*_dependencies=.*$",
+        "^.*ynh_install_app_dependencies.*$",
+        "^.*ynh_install_extra_app_dependencies.*$",
+        "^.*ynh_remove_app_dependencies.*$",
+        r"^.*\$\(ynh_app_setting_get.*$",
+        r"^.*ynh_secure_remove .*\$final_path.*$",
+        r"^.*ynh_secure_remove .*\$datadir.*$",
+        "^.*ynh_backup_before_upgrade.*$",
+        "^.*ynh_clean_setup.*$",
+        "^.*ynh_restore_upgradebackup.*$",
+        "^db_name=.*$",
+        "^db_user=.*$",
+        "^db_pwd=.*$",
+        "^datadir=.*$",
+        "^.*ynh_psql_test_if_first_run.*$",
+        "^.*ynh_mysql_setup_db.*$",
+        "^.*ynh_psql_setup_db.*$",
+        "^.*ynh_mysql_remove_db.*$",
+        "^.*ynh_psql_remove_db.*$",
+        "^.*ynh_find_port.*$",
+        "^.*ynh_script_progression.*Finding an available port",
+        "^.*ynh_script_progression.*Backing up the app before upgrading",
+        "^.*ynh_script_progression.*Creating data directory",
+        "^.*ynh_script_progression.*system user",
+        "^.*ynh_script_progression.*installation settings",
+        "^.*ynh_print_info.*installation settings",
+        r"^.*ynh_script_progression.*\w+ dependencies",
+        "^.*ynh_script_progression.*Removing app main dir",
+        "^.*ynh_script_progression.*Validating.*parameters",
+        "^.*ynh_script_progression.*SQL database",
+        "^.*ynh_script_progression.*Configuring permissions",
+    ]
+    patterns_to_remove_in_scripts = [re.compile(f"({p})", re.MULTILINE) for p in patterns_to_remove_in_scripts]
+
+    replaces = [
+        ("path_url", "path"),
+        ("PATH_URL", "PATH"),
+        ("final_path", "install_dir"),
+        ("FINALPATH", "INSTALL_DIR"),
+        ("datadir", "data_dir"),
+        ("DATADIR", "DATA_DIR"),
+    ]
+
+    for s in ["_common.sh", "install", "remove", "upgrade", "backup", "restore"]:
+
+        script = f"{folder}/scripts/{s}"
+
+        content = open(script).read()
+
+        for pattern in patterns_to_remove_in_scripts:
+            content = pattern.sub(r"#REMOVEME? \1", content)
+
+        for pattern, replace in replaces:
+            content = content.replace(pattern, replace)
+
+        open(script, "w").write(content)
+
+    for conf in os.listdir(f"{folder}/conf"):
+
+        conf = f"{folder}/conf/{conf}"
+
+        if not os.path.isfile(conf):
+            continue
+
+        content = open(conf).read()
+        content_init = content
+
+        for pattern, replace in replaces:
+            content = content.replace(pattern, replace)
+
+        if content_init != content:
+            open(conf, "w").write(content)
+
+
+manifest = _convert_v1_manifest_to_v2("./")
+open("manifest.toml", "w").write(_dump_v2_manifest_as_toml(manifest))
+
+cleanup_scripts_and_conf("./")