Fix Makefile filenames.

According to the documentation:

https://www.gnu.org/software/make/manual/html_node/Makefile-Names.html
Merge pull request #120 from robru/patch-3

Fix Makefile filenames.
Fixes #123 by adding "internal" flag to commands (both core and custom
sandbox commands), also adds `Window:Close` command.
Merge branch 'master' into trim_whitespace