IDE 2 - Library Manager - Should not update Library linked in and/or which is a git clone

[KurtE]

Describe the request

The current library manager code. appears to want to update libraries which it did not install and/or which has been superseded by a git clone setup. Sometimes, I might do the git clone directly into the /libraries folder.
But most times I will do it into another location like: d:\github
and then I will create a link to it within /libraries folder.
like on windows: mklink /J SDFat d:\github\SDFat

And in my case, I am using the Teensy (PaulStoffregen) version of SDFat not Bill Greiman's version.

But then IDE 2 launches, comes up with a list of libraries to update including SDFat.

Request - Check for some specific hints that the libraries were not installed by the library manager and either not include these libraries in the automatic update cases or give warnings. Cases include:

a) Library code is not directly within the /libraries folder but is instead a symbolic link to somewhere.
b) The library containg git file like on windows a .git directory.

Describe the current behavior

IDE2 library update - will try to update/replace libraries that it finds in the sketches/libraries folder that I installed using
git clone. I often times clone libraries as to make source code changes to the library, and this update could potentially cause these changes to be lost.

Note: the current link (Junction on windows) case can give strange feedback/results.
For example I have JPEGDEC cloned right now with junction:

In this case: I actually have the sources for the current version: But I hit update

Not sure where it is geting the current installed version number? I have same issue with Adafruit_BusIO, where it says I have installed older version, but the library.properties file says I have the current version and the update says so as well...

Yesterday when I tried the update of another library with junction to github version,
the update failed, saying it could not rename the temporary folder to the actual library name.
It then deleted the temporary directory it unzipped the staged version to. During this process the Junction was
removed. Trying the update again then succeeded. Luckily, I don't believe the github sources were changed.

Arduino IDE version

Nightly 20220918

Operating system

Windows

Operating system version

Windows 11

Additional context

No response

Issue checklist

• I searched for previous requests in the issue tracker
• I verified the feature was still missing when using the latest nightly build
• My request contains all necessary details