I've seen that, too. For some reason the sorting sometimes doesn't ignore the text label decoration on projects.
As a workaround you could try to off the text decoration that is used to mark projects as dirty. You can use color and/or font, instead. This is in the git preferences.
I've convinced myself that this is an eclipse bug. There are various eclipse bug reports that mention issues with sorting that seem to stem from race conditions when concurrently sorting and updating the items being sorted.
The AADL navigator's list of projects often re-sorts itself during tool execution. This is confusing and visually frustrating as I lose track of my projects.
Expected and Current Behavior
The ordering of projects in the AADL Navigator view should not change if the user is not changing the projects.
Steps to Reproduce
I installed OSATE 2.3.2 vfinal and the ALISA examples. Running the SCSCase causes the navigator list to re-order itself several times.
Here's a video of the problem: https://youtu.be/tjE5eiGDBNY
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