Describe the bug
When I first installed I believe RC2 or 3 but for sure with Nightly build and started testing with the first versions of the
Teensy installs, I found I could no longer build some of the sketches I was working on.

I traced it down to the first run of the IDE, overwrote my existing libraries in my /libraries
and replaced the version I was working on.

In my Particular case it was the SD library. My current one was our current Github fork/branch of SD which is a thin wrapper to call off to the SDFat library.

Note: In my case, it was actually a symbolic link to where I keep all my sources
On my Windows machine I created this using: mklink /D SD d:\github\SD

Note: This also reproduced on my Ubuntu machine as well.

To Reproduce
Steps to reproduce the behavior:

Have some custom version of SD in your /libraries/SD
Install IDE 2
run the IDE

Also found that this will reproduce if you are having the issue, that updates in your tools.txt or tools.local.txt are not showing up as mentioned in:
arduino/arduino-cli#1614
And you delete the directory

C:\Users\<user name>\AppData\Roaming\arduino-ide\

And restart the IDE.

I noticed in the output window:

Downloading LiquidCrystal@1.0.7
Installing LiquidCrystal@1.0.7
Already installed LiquidCrystal@1.0.7
...
Downloading SD@1.2.4
Installing SD@1.2.4
Replacing SD@2.0.0 with SD@1.2.4
...

Notice it says it replaced SD and sure enough it did

Expected behavior
I would expect it to leave alone user libraries, especially ones marked with a higher version number

Screenshots

Desktop (please complete the following information):

• OS: Windows
• Version: 10
• OS: Ubuntu
• Version: 20.0.4

Additional context