The README for pg_indent says:
./configure # "make" will not work in an unconfigured tree
cd src/include/catalog
make reformat-dat-files
cd ../../..
This looks like a case of using a sledgehammer to crack a nut.
I did this, which amounts to the same thing and is faster:
cd src/include/catalog
perl ./reformat_dat_file.pl --output . ./pg_*.dat
cd ../../..
cheers
andrew
--
Andrew Dunstan
EDB: https://www.enterprisedb.com