When you restructure the website's aliases, be careful not to change nodes (pages) which were automatically imported. More specifically, all aliases under
should __never__ be touched. If you change such alias, the links to the API documentation (Doxygen) will break and lead to 'page not found (404)' error messages.
While we're at it, If you link to a node, always use node/1234 instead of the alias. In that way, when the alias changes, the link remains valid. Drupal will convert 'node/1234' to the specified alias anyway such that the user never sees a difference and always sees the alias.