Run git add multiple times when too many files to add

[deshipu]

When there are more than 1000 files to pass into the git add command, run that command multiple times, with up to 1000 files at a time, to avoid problems with too long command line.

Fixes #334

PR Description

When there are more than 1000 files to pass into the git add command, run that command multiple times, with up to 1000 files at a time, to avoid problems with too long command line.

Fixes #334

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