I am debugging a Wordpress plugin, and the development environment convention is to symlink from the wordpress plugins folder, to the git source tree folder.
Within Cloud 9, we can then perform all debugging on the Wordpress code tree - treating our plugin as just another set of wordpress files.
The problem arises when we set a breakpoint on our plugin. Cloud9 stores the breakpoint as existing within the symlinked folder, however, when the breakpoint hits, Cloud9 then resolves it back to the real file location, opening a duplicate source file.
This is a mess - because the breakpoints dont show in the actual file, setting new ones then dont work, either Cloud9 or xdebug gets all confused… etc