You are right. It currently does target the caption (specifically the place where the word `Figure' is). Targeting the exact figure is something that I will work on.
> what looked like [13] was stored as @13#.
We probably should support more citation styles. Currently only the bracket style is supported but some papers cite using parentheses or other formats. If brackets being stored as @[NUM]# turns out to be common I could handle that too but I don't know how common it is since I have never seen something like this.
>The helper window opened behind the main window (for me, anyway), which is a little awkward.
You are right, we should fix this ASAP.
>As I was reading, I found myself wanting Smart Portals more than Smart Jump. Same automatic cross-reference detection as Smart Jump, but defining a Portal instead of a link.
There is kind of an smart portal feature in the sense that if you press 'p' and then middle click on something, then sioyek creates a portal from your current location to the location that it would take you if you just middle clicked on the text.
Automatic cross reference detection without user input is something that I have thought about and definitely want to do but the problem is there may be too many false positives, which could make things annoying. For now I think the semi-smart portals are a decent compromise.
>The view in the helper window can't be zoomed or panned, so unless it's kept at the same width as the main window was when the portal was captured, the helper window tends to crop out part of the captured content.
Yes it can. If you want to adjust a portal, press 'P' (that is, shift+p) while the portal is active. This takes you to the location of portal, now you can pan or zoom in and when you are done, press backspace to get to where you were. The portal will be updated with the new zoom/pan.
> I found myself liking shift-o more than I thought I would, more than tabs. It would be helpful to be able to clear entries from the previously opened list though; mine is now littered with test files.
You are right, definitely should add the ability to delete old documents.