Fix how jprotoc handles debug output with subdirectories

[rmichela]

Fixes #104

[codecov]

Codecov Report

Merging #105 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #105   +/-   ##
=========================================
  Coverage     80.22%   80.22%           
  Complexity      239      239           
=========================================
  Files            34       34           
  Lines           799      799           
  Branches         82       82           
=========================================
  Hits            641      641           
  Misses          134      134           
  Partials         24       24

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