The way _I_ would like things to work for me (the use case 2 I was talking about) is as follow:
1) I write a document in tradional, unbundled, fashion: 'filename.lyx' 2) When I am done, I click "save in bundled format". This will generate a 'filename.lyz' file wherever I said to generate it (could be in the same directory). This bundle creation was done in two steps: a) create a [tmpdir]/filenamedir.lyxdir/ directory b) copy filename.lyx to [tmpdir]/filename.lyxdir/content.lyx c) copy layout (if not standard) and biblio to [tmpdir]/filenamedir.lyxdir/embed/ d) copy referenced files to [tmpdir]/filename.lyxdir/embed/ e) modify [tmpdir]/filenamedir.lyxdir/content.lyx so that file reference point to the corresponding files in [tmpdir]/filenamedir.lyxdir/embed/. The session info should keep a trace of the original referenced file paths. f) zip the directory filenamedir.lyxdir/ into filenamedir.lyz 3) I send this filenamedir.lyz to my reviewer. There is basically two modes of operation for the reviewer: 3-a) He only want to touch at the text contents. In this case there is no real need for him to unbundle. So LyX should automatically unzip the archive in [tmpdir]/filenamedir.lyxdir/ and open [tmpdir]/filename.lyxdir/content.lyx, this user doesn't need to know where the other files are. When saving, only content.lyx in the archive needs to be updated, simple. 3-b) The reviewer wants to touch at some of the embedded files. In this case, he should first unbundle filenamedir.lyz into current directory. This will create 'filename.lyx' directly extracted from 'content.lyx' in the archive as well as the 'filename.embed' subdirectory directly extracted from the 'embed/' directory in the archive. When the reviewer is done with his corrections/additions, he just has to click on "save in bundled format" (step 2 above) and send me back the file. 4) I receive the file and review the change in bundled mode. 4-a) If I am fine with the addition I can click on "merge with lyx file". I select the original filename.lyx file. LyX notice that there is a session for this file and proceed to the merging. For each of the embedded file that has changed, LyX should ask me whether I want to overwrite the original file. An "accept all" button could speed up this process if desired. 4-b) I want to study a bit deeper the addition so I choose to unbundle the file, see 3-b. I revert any change file that I am not happy with and then I can merge the file. Abdel