BID does use build-directories to contain all generated files. So your source directory will not be modified. If you try to configure or build your L4 system without specifying a build-directory an error is issued. Simply name an build-directory (or output directory) when calling make with the variable O set:
~> make O=/path/to/your/build/dir
To create this directory and set up a basic Makefile infrastructure in this directory you have to call first:
~> make O=/path/to/your/build/dir config