Major: EFF was mostly correct in their analysis. Using the document you posted, EFF won their battle to have NeoMedia's '048 patent narrowed. All claims in the patent were narrowed or cancelled in the first amendment at the request of the EFF.
For instance, the old Claim 1 was unclear when it claimed:
"reading a data carrier modulated with an index;"
As your source and EFF noted, it sounded as if a person could read it.
The amendment narrowed Claim 1 so that a machine had to read the code (scan the code). So if a consumer entered the UPC, it is no longer covered by the patent:
"reading with a user computing device a data carrier modulated with an index;"
The second outdated statement that "the phone paired the UPC number with a URL," was another ambiguity eliminated in the re-exam. After the re-exam the phone is not allowed to do the pairing. Instead it must be sent to a server that does the pairing. This step was added to the claim so that it would defined over the prior art in the re-exam:
"b) transmitting the index to a remote server computer over the network;" **
The next 34 claims are dependent claims on Claim 1 and so were also narrowed by claim 1, cancelled, or individually amended.
Claim 36 is the next independent claim and was amended based the prior art references supplied by the EFF. The next 34 claims are dependent claims on Claim 1 and so were also narrowed by claim 36, cancelled, or individually amended.
The third independent claim, Claim 71, was individually amended based the prior art references supplied by the EFF.
The remaining claims are dependent claims on Claim 71 and so were also narrowed by claim 71, cancelled, or individually amended.
So, the EFF document achieved its objective and therefore their document you posted is no longer a valid description of the current patent.
Then there was a second re-exam and subsequent amendments...
** This added portion of the claim is where NeoMedia runs into a problem with the SpyderLynk lawsuit. SpyderLynk does not send the index to the remote server, it sends an image of the logo and outside frame.