Fix stale resource link flags after project re-open

[trancexpress]

Whenever a project is closed, its resource tree is saved. This includes linked resources in the project. When the project is re-opened, link changes in the .project file are not reflected on the projects resource tree. The old resource tree is read, new information is stored in ProjectDescription.linkDescriptions, but the old linked resources are not touched.

This change adjusts Project.open() and Project.close() to set resp. clear the M_LINK flag of linked resources in the project.

Fixes: https://github.com/eclipse-platform/eclipse.platform/issues/470

[github-actions[bot]]

Test Results

   639 files  ±0     639 suites  ±0   38m 49s :stopwatch: - 2m 29s  3 950 tests +1   3 928 :white_check_mark: +1   22 :zzz: ±0  0 :x: ±0  12 456 runs  +3  12 295 :white_check_mark: +3  161 :zzz: ±0  0 :x: ±0 

Results for commit fc5d071b. ± Comparison against base commit 1012283f.

:recycle: This comment has been updated with latest results.

[trancexpress]

I'm not sure if this is a good fix, code-wise it doesn't seem like a good change. So far I don't have an idea how a good fix would look like. But lets see how test results look like.

[akurtakov]

What is the status of this one?

[iloveeclipse]

What is the status of this one?

Waits for a review

[mickaelistria]

FWIW, I have trouble to properly understand the use-case. @trancexpress would it be possible to add a test that would demonstrate how to trigger the issue?