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lrwxr-xr-x 35 Jun 3 2023 glcc -> ../gigatron/gigatron-lcc/build/glcc
lrwxr-xr-x 36 Jun 3 2023 glink -> ../gigatron/gigatron-lcc/build/glink
lrwxr-xr-x 38 Oct 21 11:02 gt1dump -> ../gigatron/gigatron-lcc/build/gt1dump
lrwxr-xr-x 40 Jan 1 09:39 gt1z -> ../gigatron/gigatron-rom/Utils/gt1z/gt1z
lrwxr-xr-x 37 Jun 3 2023 gtprof -> ../gigatron/gigatron-lcc/build/gtprof
lrwxr-xr-x 36 Jun 3 2023 gtsim -> ../gigatron/gigatron-lcc/build/gtsim
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PATH=$HOME/bin:$PATH
In principle, "make clean" in glcc only cleans what is in the build directory, and in fact completely removes it. So in short, you should never put anything precious into the build directory. But I frequently create subdirectories in the "gigaton-lcc/stuff" directory for various programs, and they are not disturbed when glcc is recompiled from scratch.
For you particular versioning problem, you could just remove the glccver.py file that is in the build directory. But frankly there may be plenty of other problems. Best would be to delete the build directory completely and compile from fresh.