MT alt-trans is put in the same file in case of sub-folders with same filenames

[ysavourel]

When the project has sub-folders and two input files (in different folders) have the same name, the alt-trans MT entries of the last file processed overwrite the one of the previous file.

We need to create the sub-folder structure in the tm/mt folder too. (If OmegaT allows sub-folders)

[ysavourel]

Changed to use relative path for alt-trans TMs and glossary. This resolves issue #3.

→ <<cset 29de410bf4d5>>