New installs overwrite existing libraries in the <sketchbook folder>/libraries

[KurtE]

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

[ubidefeo]

hey @KurtE

I'll bring this into our triaging, seems like a pretty annoying one.
Might be a regression introduced when we enabled first-install bundled libraries installation.

Thank you for reporting ✌️

[per1234]

The same happens with the first run "Arduino AVR Boards" installation (#497):

1. Use "Boards Manager" to install a previous version of the "Arduino AVR Boards" platform.
2. Select File > Quit from the Arduino IDE menus.
3. Rename or delete (:warning: cautiously) the following folder to simulate a first run of Arduino IDE 2.x:
   • Windows:

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

   • Linux:

     ~/.config/arduino-ide
     

   • macOS:

     ~/Library/Application Support/arduino-ide
     

4. Start the Arduino IDE.

The IDE will now upgrade the "Arduino AVR Boards" platform from 1.8.4 to 1.8.5.

Upgrading platform arduino:avr@1.8.4 with arduino:avr@1.8.5

Some users may have been intentionally using a specific version of the platform with Arduino IDE 1.x in order to provide a controlled dependencies environment for their projects. They would likely not appreciate the IDE 2.x doing a silent upgrade when they make the migration.

[PaulStoffregen]

Is this issue still present in 2.0.0-rc7? (tagged "criticality: highest" in February)

[kittaakos]

I propose to check if this can be reproduced with the CLI only:

• wipe #directories/data and #directories/user/library,
• install a patched SD lib into #directories/user/library manually (verify you can use the library, compile!)
• install the AVR core with the CLI (no gRPC), and check if the SD was overridden.

Check if the AVR core has to be installed. The corresponding code is here.