Discovered while solving #1315.
Reproducible with steps:
mkdir repo
cd repo
git init
mkdir foo
touch main.c
git add .
git commit -m "commit"
Then run the indexer with an -i main.c switch to ignore such file. Investigating the data directory, there is a record for main.c in the historycache.
I believe the same works for acceptedSymlinks as the code lacks this code as well.