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removeUnusedTreeFiles shared one exclude list across all projects. removeFiles drops a name from it once it sees the matching file, but when a project had no tree file on disk its name stayed in the list. Tree files are named by a per resource sequence number, so that leftover name can match an outdated tree file of a later project and keep it from being deleted. Build the exclude list per resource instead. Contributes to eclipse-platform#2887 Assisted-by: multiple AI agents and layers of automated tooling 🤖
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During a workspace save, removeUnusedTreeFiles deletes outdated tree files of the workspace root and every project, but it carried a single exclude list across all of them. When a project had no tree file on disk, its file name stayed in that list, and because tree files are named by a per resource sequence number it could match an outdated tree file of a later project, which was then never cleaned up. The exclude list is now built per resource, so each project only protects its own current tree file.
Contributes to #2887