All your user created bookmarks will be stored in .Shared file.
I'm not sure if it takes 100MB to store a bookmark.
May be your shared files are corrupted.
I would first take proper backup.
Try by deleting .Shared file and check if this resolves.
By deleting .Shared file all the user created objects will be deleted too.
In this case you can restore the same from backup file.
Hope it helps