Bring back (again) bootstrap.sh executable bit

Reverts "bootstrap.sh: cannot keep exec bit on windows" commit
2d2eca18b8c326f1e3ea9101d00b3370c8c5c290.

We do not need to remove executable bits to workaround old msysGit bug that
shows files having executable bits as modified.

This can and should be addressed by msysGit user either by using latest version
that will treat `bootstrap.sh` as having executable bit because of UNIX Shebang
presence, or setting Git config's `core.fileMode` to false.

See:

http://stackoverflow.com/questions/12193020/file-mode-with-msysgit
http://www.grumpydev.com/2011/01/19/switching-from-cygwin-to-msysgit-git-thinks-everything-has-been-modified/

Quoting Git manual:

  core.fileMode
      If false, the executable bit differences between the index and the
      working copy are ignored; useful on broken filesystems like FAT.
      See git-update-index(1). True by default.

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