fix: Smudge non-annexed files, ensuring eol enforcement

[effigies]

This patch should avoid further pollution of repositories with CRLF end-of-line markers. What seems to be happening is that git annex add ensures that we efficiently hash files, but does not ensure that non-annexed files pass through the smudge filters. Adding a second add_all should be a cheap fix for this.

I also skip empty commits.

With these two changes, I think the following would fix old datasets: git_commit(repo, '.', message='[OpenNeuro] Apply smudge filters'). I'm not sure if this is something that should be put onto the task queue?

Fixes: #3257
Fixes: #3531

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 45.02%. Comparing base (380c6ee) to head (937d9ca).
⚠️ Report is 13 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3664      +/-   ##
==========================================
+ Coverage   42.99%   45.02%   +2.02%     
==========================================
  Files         636      636              
  Lines       33912    33922      +10     
  Branches     1516     1595      +79     
==========================================
+ Hits        14582    15274     +692     
+ Misses      19191    18519     -672     
+ Partials      139      129      -10     

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