Thanks.
I suggest adding another table:
CREATE TABLE w3t_Mods_Files (
M_ID int(11) NOT NULL default 0,
M_File varchar(255) NOT NULL default '',
M_New char(1) NOT NULL default '0',
KEY M_ID (M_ID),
KEY M_File (M_File)
);
This table keeps track of which files were added (M_New = '1') or modified (M_New = '0') by each mod.
Each row of the table contains one filename, so if a mod affected ten files, then there would be ten rows.
Then by doing the appropriate query, you could obtain a list of all files related to a specific mod, or a list of all mods that affect a specific file.