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When using a project connected to a Rational Team Concert repository, clicking on a make target in a sub directory invokes the make command in some random place. Most time it invokes $(HOME)/Makefile if it exists, but sometimes it also starts the make command in an arbitrary directory. Invoking a make target in the root folder of a project works as intended. Also, if the project is disconnected from RTC, the make target view works as expected. RTC installs its own EFS which has URIs like sourcecontrol://jazz/default/ This problem could be similar to these ones: https://bugs.eclipse.org/bugs/show_bug.cgi?id=378703 https://bugs.eclipse.org/bugs/show_bug.cgi?id=378882