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fix(clone): reset index of YADM_WORK #492

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AVM-Martin
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What does this PR do?

Whenever using clone command inside YADM_WORK sub-directory, we need
to checkout the correct repo contents.

Steps to reproduce:

mkdir $HOME/subdir
cd $HOME/subdir

yadm clone --bootstrap "<repo-url>"
yadm status

What issues does this PR fix or reference?

[A list of related issues / pull requests.]

Previous Behavior

yadm status reported a lot of deleted files.

New Behavior

yadm status will report clean working directory.

Have tests been written for this change?

Yes

Have these commits been signed with GnuPG?

Yes


Please review yadm's Contributing Guide for best practices.

Whenever using `clone` command inside YADM_WORK sub-directory, we need
to checkout the correct repo contents.

Steps to reproduce:

```bash
mkdir $HOME/subdir
cd $HOME/subdir

yadm clone --bootstrap "<repo-url>"
yadm status
```
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