We're trialling a new system on our beta server that allows advanced users to more finely customise their email filtering rules.
The problem with the current approach is that it's "all" or "nothing". If you start editing the sieve script to make it custom, then you have to keep editing it as a custom script, you can't have most it generated by the Define rules screen, with just a few custom rules inserted at the points you want.
Also, over time we've added certain features that have required inserting rules into your generated script. For instance, when you use Distribution Lists and use the "Archive into folder" option, that works by bcc'ing you on every email to a special address. We insert a rule into your sieve rules to match those emails, and file it into the folder you selected. If you're using a custom script, then that rule isn't generated, and thus you might end up with emails in your Inbox that you don't expect to see.
The way the new system works is that instead of having a "custom script" option, there's now an "Advanced" tab on the Define Rules screen. On that tab, there's a single textarea editor. The content of that area is treated specially as "blocks". Each block has a special format, and it allows you to insert the content of the block into various parts of the sieve generation process.
For more information on how this works, we’ve documented the process on the wiki:
Remember all of this is currently very experimental, and subject to significant change based on feedback.