I've done this in the past for a project. I think the issue is there's a maximum width of the MANIFEST.MF file. You need to ensure that any changes you make stay within the width of the file Talend's generates.
Also, be careful with this approach if you start sharing the lib folder in particular: I found that, later, when I wanted to update one of the jobs using the shared jars, but using a later version of the studio than I'd originally used, the new job would not play nicely with the shared jars because some of those had been updated (new/changed/removed methods).