The problem seems to be from having tup running in a subdirectory of the 
git repo -- a valid scenario.
( setting GIT_DISCOVERY_ACROSS_FILESYSTEM before running tup did not help)
Here is a script that replicates the problem:

#!/bin/bash
# how to get "fatal: Not a git repository "
# Probably caused by working in a subdir of the root git
#

mkdir tuptest && cd tuptest
mkdir src
git init
touch src/main.cpp
git add src/main.cpp && git commit -m "first"
cd src
tup init
cat > Tupfile << "EOF"
COMMIT_ID=`./get_commit_id`

: main.cpp |>  g++ -DCOMMIT_ID=$(COMMIT_ID) -c %f -o %o |> %B.o
EOF

cat > get_commit_id << "EOF"
#!/bin/bash
COMMIT_ID=`git log -1 --oneline | cut -d\  -f 1`
echo $COMMIT_ID
EOF
chmod +x get_commit_id
tup upd


On Wednesday, December 28, 2016 at 7:42:26 PM UTC+2, Andrew Jensen wrote:
>
> I have never had issues with tup "accessing the file system" as you say in 
> your PS above. I have not been able to reproduce your issue even with 
> variants.
>
> However, I can reproduce the issue if those tup files are not inside a git 
> repo. Are you sure you did a git init?
>
> If you are still having issues, please give a complete step by step 
> procedure to reproduce, starting with an empty directory and no git repo. 
> The steps should include creating the git repo and initializing tup, as 
> well as the contents of each file you create.
>
> -Andy
>
>

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