The publishing procedure number 2 is the more aggressive one with respect to using the Linköping University Electronic Press. Its basic idea is that the author publishes the first version of his/her article in the E-Press as soon as it is ready, and then submits it to journal or conference reviewing afterwards. This is clearly acceptable for some journals/conferences; it is likely to work fine for workshops in most cases; it is the only mode of operation for the new European AI publishing system (Electronic Transactions on Artificial Intelligence); it is almost certainly OK with IEEE and has a good chance of being OK with ACM, and it is almost sure to preclude external publication in some journals or conferences.. The user of this procedure must therefore be careful to know what he/she is doing.
To use procedure 2, one proceeds in the following steps:
If the publisher is IEEE, you are required to replace the previous electronic version of the paper with the new one. The E-Press will comply with this requirement by storing the revised version of the article in the URL where the original version was stored before, and move the original version to another URL. However, both the original and the revised version will be accessible from the cover page.
We do not recommend to republish the revised version of the article as a separate E-Press publication, because of the complications that that may entail.
The author confirms and ACM (resp. IEEE) accepts that the preliminary version of this article has previously been published, without refereeing, by Linköping University Electronic Press, and that they have a right to keep the original version of the article on-line on the Internet, provided that a clear citation of the definite publication by ACM (resp. IEEE) is made.
Then see what will happen; probably nothing happens. However if the publisher comes back and says that you have to remove that clause otherwise they will not publish your paper, then you must not go along; you have to abstain from having the paper published by them. This is the risk you are running with this publication procedure. - However, in the unlikely event of this happening, we recommend that you anyway include the article in your CV, explaining that it was accepted based on refereeing but then this other thing happened.
In any case, be sure to retain two copies of the copyright agreement that you signed and sent in, (or of your own, written note that you never signed any agreement), and to give one of those copies to whoever in your department is in charge of administrating copyright agreements. Starting 1997, this has to be done on the departmental level.