Err... maybe a silly question, but did you somehow change the owner of the files to someone other than you (root, perhaps)?
I'm not sure.
I typed sudo nautilus to use nautilus with root access, and placed the tech tree in /usr/share/glestae/techs.
Oh... that's why. In that case, I think you probably did scramble your permissions. sudo has a bad habit of doing that. Since it's a root operation, the end product (in this case, the new files) are under root's ownership, which means they can only be executed under root's permission. ~/.glestadv/addons is there basically so that you don't have to use root to add mods, and so all your permissions stay intact. Just for clarity, I'm talking about /home/<your_name>/.glestadv,
not /usr/share/glestae.
Here is what I would do:
1. Check who owns usr/share/glestae/techs/everything/ (or whatever you called the new folder).
http://yfrog.com/n3screenshot3qtsp2. Play GAE as root. If it works, it will assure that it is actually a permission problem and not something else.
3. As yourself (not root), move the relevant tech tree files to ~/.glestadv/addons/. Since you're doing it as yourself, it should make you the owner of the new files.
4. After that, you should be able to (as root) remove the unneeded remnant in /usr/share/glestae. This should not be strictly necessary, but you don't really need an extra couple gigs of clutter lying around.
5. Instead of 3 and 4, you may be able to change the owner of all the files in /usr/share/glestae/techs/everything/ from root to yourself, but I don't exactly know how to do that or if it would actually work.