There are some permission issues with copying an existing dokuwiki filesystem to a new Webfaction install (this may also be an issue with other hosting companies). The problem occurs when the existing file permissions are incorrect, i.e., the files are not owned by the webserver. The solution to this is to change permissions to apache:username where username is your ssh user account.
Assuming the file permissions were set correctly in your previous dokuwiki installation and these were retained you would expect to do this using standard Unix commands:
chown -R apache:username ~/webapps/dokuwiki/data/pages
However, chowning will throw a number of errors similar to this:
chown: changing ownership of `start.txt': Operation not permitted
The problem of changing the ownership of a file or directory to the webserver is well understood and the good people at Webfaction have developed a solution (documented here and here).
By executing the following command it is possible to make a directory or file writable by apache:
setfacl -R -m u:apache:rwx /path/to/whatever
To make the contents of dokuwiki's pages directory writable by Apache on Webfaction execute the following:
setfacl -R -m u:apache:rwx ~/webapps/dokuwiki/data/pages