System calls to gitlab-shell were using unsanitized user input

Migrate notes.line_code format.

Since version 4.1, notes.line_code means:
  {SHA1 hash of file path}_{old line}_{new line}
but the older version means:
  {file index of the commit}_{old line}_{new line}

This rake task migrate the above differences.

Update init.d script

The original init.d script uses a fixed username (e.g. git). Which is not flexible
when we using other user. So, I've updated it to use $APP_USER variable
instead and wrap it in a function to reduce repetitive codes.

Fix not using git.bin_path in config.

Add Gitlab::VersionInfo class to fix and simplify version check.

improve gfm autocomplete

It returns "yes" if required version is "1.7.10" and current version is "1.6.10",
because the patch version of current version equals to that of required version.

Setting the working directory before git operations

Puma configuration for relative base URL

Bump charlock_holmes to 0.9.6.4

Signed-off-by: Axilleas Pipinellis <axilleas@archlinux.gr>