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Hi elpidiovaldez,
You have this directory structure because you have used catkin_build
(build and install) and catkin_build_isolated
(build_isolated and install_isolated) in this workspace. You should use only one.
catkin_make
treats the entire workspace as a single cmake project, and builds it with a single invocation of cmake. Since catkin_make treats the entire workspace as a single package, it's faster for incremental builds that only change code, but slower when you need to regenerate the build files, and more sensitive to dependency issues between packages.
catkin_make_isolated
treats each package as a separate cmake project, and builds and installs each separately, in dependency order. This is why it's able to build plain cmake packages.
You can find more detail in this thread
If you want to build only your package try to run:
catkin_make_isolated --pkg <your package name>
for more usefull arguments and/or options:
catkin_make_isolated -h
Regards