improve installer script

refs #7312

Do not change permissions on files that are not created by the
storage service.
increase default timeout values

refs #7311

The storage service uses nginx by default as a web server. The default
timeout values are 60 seconds in nginx.  This change increases
those timeout values to 1 hour.  This allows Archivematica to POST
large files (e.g. large AIP's) to the Storage Service.