When a C/C++ project is created for ESbox, most projects will have autotools and Make builders assigned. The autotools builder will run autogen.sh or autoconf and then the generated configure script. The Make builder, will then run make on the generated or pre-written top-level Makefile in the project.
The Make builder may be configured for the project so that other Makefiles can be invoked or other targets can be selected for common Eclipse build actions. Consult the Project > Properties > C/C++ Build Settings page to see the settings.
Build location is the location, typically relative to the project, where the build command is launched. You may use this to build inside a large project, for instance. Note: this also affects the autotools builder.
When a project is imported from a Debian project, only a Make builder is used, and fakeroot debian/rules is used as the Build command. This file will itself run autotools commands, so the Project > Build Application menu will not provide the autotools-related commands.
Rules selected for Build and Clean build types are derived from the Debian policy manual. If your project does not use these rules, you must edit them here.
If you wish to de-Debianize a project, check Use default for the Build command. You may also need to convert the project to use the Autotools builder.