Git and automatically generated files

I am looking at the file Makefile.gen inside gr-trellis/src/lib
which says that is automatically generated.
This is indeed true since when i delete it and make
gr-trellis it correctly generates it with all additions, etc
that are implied by the file generate_trellis.py

However if I delete it and try to do ./bootstrap (on the whole project)
then automake reports an error
automake: cannot open < gr-trellis/src/lib/Makefile.gen: No such file
or directory

I came across this issue when i decided to put Makefile.gen in the
.gitignore and not track it
since it is machine generated…

What is the explanation of this behaviour?
Shouldn’t all automatically generated files not be tracked by git?

thanks
Achilleas

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