Added creation of pids directory to fix #2995, replaced deprecated nginx init.d command with service one, some more clean-up

Instead of using funtion `error!` the function `not_found!` is used to return 404 error. Adjusted documentation accordingly.

Made it a bit clearer what step 5 is for to stop people skipping it. This time with a relative link.

The API version is currently not equal to the gitlab major version number. Gitlab 4.1 
still uses API version 3. Point to the lib/api.rb file instead which contains the
autoritative information.

Change "th" to "the"

'th -> the' typo