Packages break and I keep restarting

Hello,

I'm sure I'm not the only one with that issue and I did hestitate to write anything about it in here for long but the issue keeps coming back and I dont know what I am doing wrong.

Yesteday I did reset my git project to a older version (around 6 weeks back) to test updating the player with squirrel. Today I updated git to the current status and the console was spammed with HDRP errors, precisely:

System.Exception: Cannot load. Incorrect path: Packages/com.unity.render-pipelines.high-definition/Runtime/RenderPipelineResources/ShaderGraph/AutodeskInteractive.ShaderGraph Null returned.
...

So I did restart Unity a couple of times hoping it would resolve broken packages as it did in the past. It didnt help this time.
Then I read on SO that it might help to remove the Scriptable Core, ShaderGraph and finally HDRP and then reinstall just HDRP which would then resolve its dependencies so I did just that.
I installed the same HDRP version as before and package manager said its dependencies SR-Core and ShaderGraph are installed (although they didnt show up in the "Packages/In Project"). So I switched to all packages and manually clicked install on SR Core and ShaderGraph again. Restarting Unity. Same error as before, so nothing changed.
At first i tried to just delete the HDRP, ShaderGraph and SRCore packages in "<MyProject>\Library\PackageCache" and restart but that didnt change anything.
I then went into "C:\Users\<user>\AppData\Local\Unity\cache\packages\packages.unity.com" AND "<MyProject>\Library\PackageCache" to manually delete cached packages. Restarting Unity once - some packages were resolved and I suddenly got errors about a missing Autodesk namespace. I didnt touch any Autodesk or FBX Packages so I tried to restart a couple more times but the error didnt go. I then deleted the Autodesk.fbxand unity.formats.fbx packages in both directories mentioned above and voila: all errors gone.

So my problem with this is:
I dont know why my packages broke in the first place through resetting git to a previous version - package caches should be unaffected by that, right? Especially those in AppData?
And then I would love a package manager option to "clean caches" or at least have a "fresh install" button to NOT use broken (?) packages in a cached folder.
Oh and while I'm at it: Why do I have to restart unity so often when working with new packages for the first time? Like HDRP... I never know for sure if the error is just something isnt quite resolved yet or there is still something missing and that is a bit frustrating to say the least.

Working with 2019.1.6f1 on this particular project if that's relevant.

 

Hello Erick, thanks for the reply. Sure no problem.

 

I haven't edited the manifest manually and just asked my team who confirmed: they also haven't edited the manifest file directly