If you go back and read my previous response, the main reason I removed the option to write annotations to the underlying PDF automatically is that a lot of users did enable that setting (it was off by default), they made massive permanent changes to their files without realizing the consequences of this and I had to spend a lot of time dealing with the customer support, taking away from development time. As mentioned previously, once you embed the annotations, you lose out on a fairly large number of features, and there is no undoing this, as you've modified the underlying PDF itself. I'm subject to what the PDF specification allows, and what the PDF library I'm using supports on top of that (it is far from bug-free). For example, I was not able to embed font-based stamps as it would crash the PDF library with memory corruptions, so I had to resort to embedding them as images. Font-based stamps can be resized without a loss in quality while images cannot.
There were also rare issues with some users where the annotations that were embedded in their files got corrupted, most likely due to some race condition that I was never able to reproduce. One of these users had hundreds of annotations per page, so it was a huge ordeal. You are the only user to request that this option be added back in the last two and half years since it was removed, so it does not appear to be a big issue for the vast majority of users. If many users chime in on this thread indicating that they really need this feature to be added back, then I can consider doing so. I just opted for the solution that provided the most reliability, as I didn't want to take any risk of users' annotations being corrupted.
You may point out that many PDF editors don't have any of these issues with writing annotations into the underlying PDF. Those editors are limited by what the PDF specification will allow though. For example, unless I'm mistaken, or there is an editor which will modify the underlying PDF content stream (meaning it becomes uneditable), you can't have highlights that go behind the page content. Also, as I mentioned previously, I support annotations on file types other than PDFs such as images and text/chord pro files. You can't embed annotations in an editable fashion in those files.
Mike
There were also rare issues with some users where the annotations that were embedded in their files got corrupted, most likely due to some race condition that I was never able to reproduce. One of these users had hundreds of annotations per page, so it was a huge ordeal. You are the only user to request that this option be added back in the last two and half years since it was removed, so it does not appear to be a big issue for the vast majority of users. If many users chime in on this thread indicating that they really need this feature to be added back, then I can consider doing so. I just opted for the solution that provided the most reliability, as I didn't want to take any risk of users' annotations being corrupted.
You may point out that many PDF editors don't have any of these issues with writing annotations into the underlying PDF. Those editors are limited by what the PDF specification will allow though. For example, unless I'm mistaken, or there is an editor which will modify the underlying PDF content stream (meaning it becomes uneditable), you can't have highlights that go behind the page content. Also, as I mentioned previously, I support annotations on file types other than PDFs such as images and text/chord pro files. You can't embed annotations in an editable fashion in those files.
Mike