Problems after updating to 7.1.3

I upgraded to 7.1.3 and have really made a big mess, a lot of the files in the db became corrupted, entire dirs exist but no one can access them. I tried running seafile-fsck and it returned that a lot of issues and said there was no previous version (or something like that, this was 2 weeks ago) trying to fix this today i did


> mysqlcheck -u root -p --auto-repair -c -o --all-databases

...

**and it returned the following many times over** 
...
$ mysqlcheck -o --all-databases
blog.users
note     : Table does not support optimize, doing recreate + analyze instead
status   : OK
...
**But now when i try to start seafile it cant connect to mysql. within mysql i can still see my dbs, but its acting like they dont exist.**
...
mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| ccnet_db           |
| information_schema |
| mysql              |
| performance_schema |
| seafile_db         |
| seahub_db          |
| sys                |
+--------------------+
7 rows in set (0.01 sec)
...

**my seafile.log**
...
> [04/29/20 17:18:06] http-server.c(235): fileserver: max_index_processing_threads= 3
> [04/29/20 17:18:06] http-server.c(257): fileserver: cluster_shared_temp_file_mode = 600
> [04/29/2020 05:18:06 PM] ../common/mq-mgr.c(54): [mq client] mq cilent is started
> [04/29/2020 05:18:06 PM] ../common/seaf-db.c(124): Failed to get database connection: Failed to connect to MySQL: Can't connect to MySQL server on '127.0.0.1' (115).
> [04/29/2020 05:18:06 PM] ../common/seaf-db.c(124): Failed to get database connection: Failed to connect to MySQL: Can't connect to MySQL server on '127.0.0.1' (115).
...

**Any ideas?**

I figured out the mysql problem, i had

[mysqld]
skip-grant-tables = 1
plugin-load-add = auth_socket.so

enabled in the conf, which stopped mysql from listening.

I still have the corrupt dir problems though