Fix hooks and documentation to alter source path

I don't think a new alter hook is needed, I just think there's a bug here.

The documentation for $context['source'] on hook_pathauto_alias_alter() states "This can be altered by reference." That is true, altering there will save an alias with a different source. However, re-saves of the same entity will create multiple aliases because the source hasn't been altered when checking for an existing alias.

Moving that documentation to hook_pathauto_pattern_alter() and passing $source by reference to that hook works through multiple saves.