Awful Charlie, you may be using an old version of SkyDemon and you will note a different user interface if you upgrade. That's assuming you're using iOS/Android. If you're using a PC, all you have to do to clear the list is Route -> New.

Julian, if only it were that easy. Categorisation of documents is done by our own software based on document names; there is no EAD metadata. We could attempt some sort of parse and alphanumeric sort but this would need to be different for each country, as there is no naming standard for these documents. Some countries put no numbers on at all. Some put three numbers, like you've pasted above, but with varying delimiters. Many do something in between. We could change the way we do things to lump all IFR stuff into one category but I would worry that would upset people who are accustomed to our current behaviour.

So the order I see for EDDK is:

3-1-1 to 3-1-2 STAR
5-7-1 to 5-7-17 SIDs
5-8-1 Minimum noise
DFS Approach chart
DFS Arrival Chart
DFS VFR Terminal chart
3-1-3 to 3-1-6 GPS Overlay of transition to final approach charts
4-2-1 to 4-6-6 Instrument Approach Charts
5-7-4 to 5-7-18 GPS Overlays of SIDs
DFS Aerodrome chart
AIP Aerodrome chart
Textual Info

I'd settle for an alphanumeric sort.   If 5-7-4 to 5-7-18 were not split from 5-7-1 to 5-7-17 it would be a significant improvement.  

How do you differentiate between a SID chart and GPS Overlays of SIDs, which are common in the German AIP. In fact more generally, how do you tell which group to put it in?  Is there EAD metadata? I'm thought I've seen approach charts out of order too, but that might be my imagination.

Not the same, but a related problem:
Having planned a route, I then go looking for alternates, which means considerations for runways, fuel, opening hours, maybe customs etc. This normally means viewing the AIP plate, so right click what appears to be a suitable airport, "Find Plates", pick off the textual information, review it, and then all too frequently, right click another airport and repeat.
Problem is I end up with a massive list of airports and plates, and the only way I've found to get rid of all the excess is to close SD & restart

For the problem the OP has, how about grouping by VFR and IFR, (as in a collapsed list with a "+" or similar to expand) and then by type (eg SID/STAR/IAC/other), as in flight I'm most likely arriving (don't care about SIDs) or departing (don't care about STARs or IACs) if VFR I don't care about IFR etc. Maybe the appropriate VFR or IFR group could be expanded by default depending on which mode the map is in?

At the moment the groups are SID/STAR Charts, VACs, IACs, Aerodrome Charts, Parking Charts and Textual Information. Within each group the items are sorted alphabetically.

What you're seeing at Cologne is (I think) the separation of the SID/STAR charts and the IACs. Suggestions welcome, given what we are already doing.

I like the Airfields tab but…

Some airfields have a lot of plates.  Cologne, for example, has 44. The ordering in the index doesn't seen consistent: there are groups that seem to be sorted by title but there are many groups, so for example 3-1-3 appears below 5-7-3 which is below 3-1-1 (with many intervening, such as the DFS Approach chart).

As a minimum, could you sort by title please?  Ideally, could you allow preselection of plates that are expected to be used, e.g. by putting them at the top of the list?

Julian