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Clean up file output handling

Merged Jim Schubert requested to merge fix-path-cleaning-on-write into master

This attempts to normalize all generators to use OS agnostic File.separator.

It also fixes a bug in some areas in code where we replace "." in full file output path with File.separator. We should only be modifying directory names we own, and should avoid modifying anything that can be provided by a user.

It would probably be better to use Paths.get(…).toString() in all cases.

PR checklist

  • Read the contribution guidelines.
  • Ran the shell script under ./bin/ to update Petstore sample so that CIs can verify the change. (For instance, only need to run ./bin/{LANG}-petstore.sh and ./bin/security/{LANG}-petstore.sh if updating the {LANG} (e.g. php, ruby, python, etc) code generator or {LANG} client's mustache templates). Windows batch files can be found in .\bin\windows\.
  • Filed the PR against the correct branch: master, 3.4.x, 4.0.x. Default: master.
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