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For synchronization projects, pressing browse during run configuration in the "Application" tab places the user in their home directory rather than in their project directory.
I have modified the application tab so that it will attempt to use the location of the project as the starting directory when browsing for the executable. For sync projects, this will be the sync location of the active configuration. However, the connection used by the resource manager specified in the launch configuration is independent of that used by the synchronized (or remote) project, so there is no guarantee that this directory even exists on the target system. In this case, it will default to the current working directory of the RM connection (usually the home directory of the user). The situation where the sync (or remote) project connection is different from the RM connection should probably be flagged as an error since it doesn't make much sense. Please open a separate bug if you think this would be useful. Note that this fix is in HEAD only as it requires an API change.