.deps/filename gets created during building with --enable-dependency- 
tracking and should get removed by make clean. But it does not. For example:

main.h:

int helloworld();

main.c:

#include <main.h>

int helloworld()
{
    return 0;
}

int main()
{
    helloworld();
}

Set up a minimal Makefile.am and configure.ac to build this. Building this  
will create .deps/<filename> with a:

main.o: main.h main.c

Now: 1) 'rm -f main.h"  2) Remove the #include

Then try to build this:

make clean
make

Will fail because that dependency exists and make does not know how to build  
main.h. I have to rm -rf .deps myself.

automake 1.16.5