[Bug]: - Githubissues

⚠️ This issue respects the following points: ⚠️

[X] This is a bug, not a question or a configuration/webserver/proxy issue.
[X] This issue is not already reported on Github (I've searched it).
[X] Nextcloud Server is up to date. See Maintenance and Release Schedule for supported versions.
[X] I agree to follow Nextcloud's Code of Conduct.

Bug description

After updating to 23.0.3, code integrity check fails with extra files, files with wrong hash, and missing files.

Steps to reproduce

1 Since I could not get the web based updater to work, timed out during backup, I. 2.initiated php occ upgrade from command line, but it told me I was already at the latest but I wasn't, so

I then typed php updater/php.phar and let it go through it's process.
When it finished, I ran a check from the settings panel and it fails code integrity check with extra file, a file with bad hash, and missing files.
I don't know how to recover and your documentation was less than helpful.

Expected behavior

Expect to start from web based updater and have it finish for once without trashing the entire system.

Installation method

Manual installation

Operating system

Debian/Ubuntu

PHP engine version

PHP 7.4

Web server

Apache (supported)

Database engine version

MariaDB

Is this bug present after an update or on a fresh install?

Updated to a major version (ex. 22.2.3 to 23.0.1)

Are you using the Nextcloud Server Encryption module?

No response

What user-backends are you using?

[X] Default user-backend (database)
[ ] LDAP/ Active Directory
[ ] SSO - SAML
[ ] Other

Configuration report

php occ config:list system
{
    "system": {
        "instanceid": "***REMOVED SENSITIVE VALUE***",
        "passwordsalt": "***REMOVED SENSITIVE VALUE***",
        "secret": "***REMOVED SENSITIVE VALUE***",
        "trusted_domains": [
            "nextcloud.eskimo.com"
        ],
        "datadirectory": "***REMOVED SENSITIVE VALUE***",
        "dbtype": "mysql",
        "version": "23.0.3.2",
        "overwrite.cli.url": "https:\/\/nextcloud.eskimo.com\/",
        "overwriteprotocol": "https",
        "dbname": "***REMOVED SENSITIVE VALUE***",
        "dbhost": "***REMOVED SENSITIVE VALUE***",
        "dbport": "",
        "dbtableprefix": "oc_",
        "mysql.utf8mb4": true,
        "dbuser": "***REMOVED SENSITIVE VALUE***",
        "dbpassword": "***REMOVED SENSITIVE VALUE***",
        "installed": true,
        "user_backends": [
            {
                "class": "OC_User_IMAP",
                "arguments": [
                    "mail.eskimo.com",
                    143
                ]
            }
        ],
        "maintenance": false,
        "data-fingerprint": "15c5e08aba95f4a9f58603c46b0bedc9",
        "mail_smtpmode": "smtp",
        "mail_smtpsecure": "ssl",
        "mail_smtpauthtype": "LOGIN",
        "mail_from_address": "***REMOVED SENSITIVE VALUE***",
        "mail_domain": "***REMOVED SENSITIVE VALUE***",
        "mail_smtpauth": 1,
        "mail_smtphost": "***REMOVED SENSITIVE VALUE***",
        "mail_smtpport": "465",
        "mail_smtpname": "***REMOVED SENSITIVE VALUE***",
        "mail_smtppassword": "***REMOVED SENSITIVE VALUE***",
        "memcache.local": "\\OC\\Memcache\\APCu",
        "memcache.distributed": "\\OC\\Memcache\\Memcached",
        "memcached_servers": [
            [
                "localhost",
                11211
            ]
        ],
        "theme": "",
        "loglevel": 0,
        "updater.release.channel": "stable",
        "ldapProviderFactory": "OCA\\User_LDAP\\LDAPProviderFactory",
        "has_rebuilt_cache": true,
        "app_install_overwrite": [
            "auto_mail_accounts",
            "caniupdate",
            "whiteboard",
            "ojsxc"
        ],
        "ldapIgnoreNamingRules": false,
        "encryption.legacy_format_support": false,
        "encryption.key_storage_migrated": false,
        "default_phone_region": "ISO 3166-2:US",
        "updater.secret": "***REMOVED SENSITIVE VALUE***"
    }
}

List of activated Apps

Enabled:
  - accessibility: 1.9.0
  - activity: 2.15.0
  - admin_audit: 1.13.0
  - afterlogic: 2.0.3
  - analytics: 4.2.1
  - announcementcenter: 6.1.1
  - appointments: 1.12.3
  - apporder: 0.15.0
  - approval: 1.0.9
  - audioplayer: 3.3.0
  - audioplayer_sonos: 1.3.0
  - bbb: 2.2.0
  - bookmarks: 10.3.0
  - breezedark: 23.2.1
  - bruteforcesettings: 2.4.0
  - calendar: 3.2.2
  - camerarawpreviews: 0.7.15
  - carnet: 0.24.4
  - cas: 0.2.7
  - checksum: 1.1.3
  - circles: 23.1.0
  - cloud_federation_api: 1.6.0
  - cms_pico: 1.0.18
  - comments: 1.13.0
  - contacts: 4.1.0
  - contactsinteraction: 1.4.0
  - cookbook: 0.9.11
  - dav: 1.21.0
  - deck: 1.6.1
  - diary: 0.0.3
  - dicomviewer: 1.2.3
  - documentserver_community: 0.1.12
  - drawio: 1.0.2
  - duplicatefinder: 0.0.13
  - eidlogin: 1.0.7
  - electronicsignatures: 1.10.1
  - emlviewer: 1.0.1
  - encryption: 2.11.0
  - end_to_end_encryption: 1.9.1
  - epubreader: 1.4.7
  - event_update_notification: 1.5.0
  - external: 3.10.2
  - extract: 1.3.3
  - federatedfilesharing: 1.13.0
  - federation: 1.13.0
  - files: 1.18.0
  - files_accesscontrol: 1.13.0
  - files_antivirus: 3.2.2
  - files_automatedtagging: 1.13.0
  - files_downloadactivity: 1.13.0
  - files_downloadlimit: 1.0.0
  - files_external: 1.15.0
  - files_fulltextsearch: 23.0.1
  - files_fulltextsearch_tesseract: 22.0.0
  - files_inotify: 0.1.12
  - files_linkeditor: 1.1.9
  - files_markdown: 2.3.6
  - files_mindmap: 0.0.26
  - files_pdfviewer: 2.4.0
  - files_photospheres: 1.23.0
  - files_readmemd: 1.2.2
  - files_retention: 1.12.0
  - files_rightclick: 1.2.0
  - files_sharing: 1.15.0
  - files_texteditor: 2.14.0
  - files_trashbin: 1.13.0
  - files_versions: 1.16.0
  - files_versions_s3: 0.1.8
  - files_videoplayer: 1.12.0
  - fileslibreofficeedit: 1.0.4
  - firstrunwizard: 2.12.0
  - forms: 2.5.0
  - fulltextsearch: 23.0.0
  - fulltextsearch_elasticsearch: 23.0.0
  - geoblocker: 0.5.4
  - gestion: 2.0.9
  - gpgmailer: 0.0.4
  - gpoddersync: 3.2.0
  - gpxedit: 0.0.14
  - gpxpod: 4.3.0
  - grauphel: 1.0.7
  - group_default_quota: 0.1.4
  - groupfolders: 11.1.2
  - groupquota: 0.1.8
  - guests: 2.2.0
  - health: 1.5.0
  - imageconverter: 1.3.2
  - impersonate: 1.10.0
  - integration_discourse: 1.0.2
  - integration_dropbox: 1.0.4
  - integration_github: 1.0.2
  - integration_gitlab: 1.0.3
  - integration_google: 1.0.6
  - integration_jira: 1.0.2
  - integration_mastodon: 1.0.2
  - integration_moodle: 1.0.2
  - integration_onedrive: 1.1.2
  - integration_openproject: 1.0.6
  - integration_reddit: 1.0.3
  - integration_suitecrm: 1.0.3
  - integration_twitter: 1.0.2
  - integration_zammad: 1.0.3
  - jitsi: 0.14.0
  - keeweb: 0.6.8
  - libresign: 2.4.5
  - listman: 20.1.1
  - logreader: 2.8.0
  - lookup_server_connector: 1.11.0
  - mail: 1.11.7
  - maps: 0.1.10
  - mediadc: 0.1.9
  - messagevault: 1.0.0
  - metadata: 0.15.0
  - music: 1.5.1
  - news: 18.0.0
  - nextcloud_announcements: 1.12.0
  - notes: 4.3.1
  - notifications: 2.11.1
  - oauth2: 1.11.0
  - officeonline: 1.1.3
  - oidc: 0.1.0
  - oidc_login: 2.3.1
  - ojsxc: 5.0.0
  - onlyoffice: 7.3.2
  - openotp_auth: 1.4.2
  - openotp_sign: 1.3.0
  - ownpad: 0.6.17
  - password_policy: 1.13.0
  - passwords: 2022.4.10
  - phonetrack: 0.7.0
  - photos: 1.5.0
  - polls: 3.5.4
  - previewgenerator: 4.0.0
  - privacy: 1.7.0
  - provisioning_api: 1.13.0
  - qownnotesapi: 21.12.0
  - quicknotes: 0.7.3
  - quota_warning: 1.14.0
  - rainloop: 7.2.2
  - ransomware_protection: 1.13.0
  - recognize: 1.12.0
  - recommendations: 1.2.0
  - registration: 1.4.0
  - richdocuments: 5.0.3
  - richdocumentscode: 21.11.306
  - riotchat: 0.11.3
  - rocketchat_nextcloud: 0.9.6
  - sendent: 1.2.11
  - sentry: 8.0.0
  - serverinfo: 1.13.0
  - settings: 1.5.0
  - sharebymail: 1.13.0
  - sharepoint: 1.11.0
  - sharingpath: 0.4.4
  - shifts: 1.8.6
  - side_menu: 2.3.5
  - signlive: 0.1.11
  - sociallogin: 4.14.0
  - socialsharing_diaspora: 2.5.0
  - socialsharing_email: 2.5.0
  - socialsharing_facebook: 2.5.0
  - socialsharing_twitter: 2.5.0
  - souvenirs: 1.3.0
  - spgverein: 0.11.0
  - spreed: 13.0.5
  - support: 1.6.0
  - survey_client: 1.11.0
  - suspicious_login: 4.1.0
  - systemtags: 1.13.0
  - tables: 0.1.1
  - talk_matterbridge: 1.23.2
  - talked: 0.3.0
  - tasks: 0.14.4
  - terms_of_service: 1.9.3
  - text: 3.4.1
  - theming: 1.14.0
  - theming_customcss: 1.11.0
  - tvshownamer: 0.1.2
  - twofactor_backupcodes: 1.12.0
  - twofactor_totp: 6.2.0
  - twofactor_u2f: 6.3.0
  - unsplash: 1.2.4
  - updatenotification: 1.13.0
  - uppush: 1.0.0
  - user_ldap: 1.13.1
  - user_oidc: 1.1.0
  - user_status: 1.3.1
  - user_usage_report: 1.7.0
  - video_converter: 1.0.4
  - viewer: 1.7.0
  - w2g2: 3.3.8
  - weather_status: 1.3.0
  - webhooks: 0.2.0
  - welcome: 1.0.1
  - whiteboard: 0.0.3
  - wopi: 3.5.10
  - workflow_media_converter: 1.3.6
  - workflow_ocr: 1.23.2
  - workflow_pdf_converter: 1.8.0
  - workflow_script: 1.8.0
  - workflowengine: 2.5.0
  - wrikesync: 1.2.9
Disabled:
  - customproperties: 2.0.4
  - dashboard: 7.2.0
  - discoursesso: 1.22.0
  - facerecognition
  - files_trackdownloads: 1.11.0
  - integration_restya: 1.0.1
  - integration_whiteboard: 0.0.14
  - openhab: 0.9.5
  - richdocumentscode_arm64
  - user_external: 2.1.0
  - user_saml: 4.1.1
  - vibeetoee: 1.2.1

Nextcloud Signing status

Nextcloud Logs

This is 20MB, I don't know how you expect me to copy and paste 20MB.

Additional info