index: Allow FileNotFoundError to be handled at the top level

[victorlin]

Description of proposed changes

The removed error handling is flawed: it assumes that FileNotFoundError can only come from a missing input file (--sequences). The reality is that FileNotFoundError can also come from a missing output directory (--output). The top-level exception handler parses the filepath from the error directly, which is accurate.

Related issue(s)

Fixes #1644

Checklist

• [x] Automated checks pass (except unrelated docs build)
• [x] Check if you need to add a changelog message
• [x] ~Check if you need to add tests~ tested locally that this works. I don't think adding a test is necessary in this case
• [x] Check if you need to update docs

[victorlin]

Updated tests in force-push.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 0% with 4 lines in your changes missing coverage. Please review.

Project coverage is 71.17%. Comparing base (bf05db8) to head (296a6c6). Report is 3 commits behind head on master.

Files with missing lines	Patch %	Lines
augur/index.py	0.00%	4 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1646 +/- ## ========================================== + Coverage 71.14% 71.17% +0.03% ========================================== Files 79 79 Lines 8273 8268 -5 Branches 2010 2010 ========================================== - Hits 5886 5885 -1 + Misses 2099 2095 -4 Partials 288 288 ```

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