Fix various small problems with configure.

- Fix temporary files not being deleted after use.
- Fix the option for disabling rpath.
- Fix the help message:
  * Fix indentation of some help options.
  * Fix default paths not containing 'run'.
  * Remove documentation for --disable-ipv6 (exists but does nothing).
  * Remove documentation for --library-dir (does not exist).
- Fix some minor errors in messages.