ENOTEMPTY when installing node from palette since nodered 3.0 (directory not empty)

I did rename the folder ".agent-base-MyGAUl8n" to ".agent-base-MyGAUl8n-OLD" but this didn't resolve anything.
Getting multiple errors trying to update, delete or install any nodes. After restarting everything I tried to install bigtimer and got the error below.

2022-08-10T17:03:05.735Z Install : node-red-contrib-bigtimer 2.8.2

2022-08-10T17:03:04.847Z npm install --no-audit --no-update-notifier --no-fund --save --save-prefix=~ --production --engine-strict node-red-contrib-bigtimer@2.8.2

2022-08-10T17:03:06.763Z [err] npm

2022-08-10T17:03:06.764Z [err]

2022-08-10T17:03:06.765Z [err] WARN

2022-08-10T17:03:06.765Z [err]

2022-08-10T17:03:06.765Z [err] config

2022-08-10T17:03:06.765Z [err] production Use --omit=dev instead.

2022-08-10T17:03:15.824Z [err] npm

2022-08-10T17:03:15.824Z [err] ERR! code ENOTEMPTY

2022-08-10T17:03:15.824Z [err] npm

2022-08-10T17:03:15.824Z [err] ERR!

2022-08-10T17:03:15.824Z [err] syscall

2022-08-10T17:03:15.825Z [err] rename

2022-08-10T17:03:15.825Z [err] npm

2022-08-10T17:03:15.825Z [err] ERR!

2022-08-10T17:03:15.825Z [err]

2022-08-10T17:03:15.825Z [err] path /config/node-red/node_modules/are-we-there-yet

2022-08-10T17:03:15.825Z [err] npm

2022-08-10T17:03:15.825Z [err] ERR! dest /config/node-red/node_modules/.are-we-there-yet-RUmkGoiI

2022-08-10T17:03:15.825Z [err] npm ERR!

2022-08-10T17:03:15.825Z [err] errno -39

2022-08-10T17:03:15.829Z [err] npm ERR! ENOTEMPTY: directory not empty, rename '/config/node-red/node_modules/are-we-there-yet' -> '/config/node-red/node_modules/.are-we-there-yet-RUmkGoiI'

2022-08-10T17:03:15.832Z [err]

2022-08-10T17:03:15.833Z [err] npm ERR!

2022-08-10T17:03:15.833Z [err] A complete log of this run can be found in:

2022-08-10T17:03:15.833Z [err] npm ERR!

2022-08-10T17:03:15.833Z [err] /root/.npm/_logs/2022-08-10T17_03_06_652Z-debug-0.log

2022-08-10T17:03:15.869Z rc=217

Delete any folders starting with a dot in node_modules.

Deleted all node_modules folders starting with a dot. All 323 of them. Restarted node-red and still getting errors. Now node-red seem to working correctly. Just can update or install new nodes.

2022-08-10T22:20:20.403Z Install : node-red-contrib-bigtimer 2.8.2

2022-08-10T22:20:19.317Z npm install --no-audit --no-update-notifier --no-fund --save --save-prefix=~ --production --engine-strict node-red-contrib-bigtimer@2.8.2

2022-08-10T22:20:20.975Z [err] npm

2022-08-10T22:20:20.976Z [err] WARN

2022-08-10T22:20:20.976Z [err] config production Use --omit=dev instead.

2022-08-10T22:20:29.346Z [err] npm

2022-08-10T22:20:29.346Z [err]

2022-08-10T22:20:29.346Z [err] ERR! code ENOTEMPTY

2022-08-10T22:20:29.347Z [err] npm

2022-08-10T22:20:29.347Z [err] ERR!

2022-08-10T22:20:29.347Z [err] syscall rename

2022-08-10T22:20:29.347Z [err] npm ERR!

2022-08-10T22:20:29.347Z [err] path

2022-08-10T22:20:29.348Z [err] /config/node-red/node_modules/@slack/web-api

2022-08-10T22:20:29.348Z [err] npm ERR!

2022-08-10T22:20:29.348Z [err] dest /config/node-red/node_modules/@slack/.web-api-iCPUJBmG

2022-08-10T22:20:29.348Z [err] npm

2022-08-10T22:20:29.348Z [err] ERR! errno -39

2022-08-10T22:20:29.352Z [err] npm ERR!

2022-08-10T22:20:29.353Z [err] ENOTEMPTY: directory not empty, rename '/config/node-red/node_modules/@slack/web-api' -> '/config/node-red/node_modules/@slack/.web-api-iCPUJBmG'

2022-08-10T22:20:29.355Z [err]

2022-08-10T22:20:29.355Z [err] npm ERR!

2022-08-10T22:20:29.355Z [err] A complete log of this run can be found in:

2022-08-10T22:20:29.355Z [err] npm ERR!

2022-08-10T22:20:29.355Z [err] /root/.npm/_logs/2022-08-10T22_20_20_873Z-debug-0.log

2022-08-10T22:20:29.380Z rc=217