I know nothing about d3, and very little about PHP, but a bit about sqlite and Apache.
For this project I'm using a minimal number of libraries, and a very simple server setup, which leads to some inefficiencies. The server is Ubuntu 14.04 with Apache 2.4 with PHP 5.6. Client side the only library I'm using is d3.js 3.5.
A consequence of the simplicity is that I don't have a good way to push data to clients, so I can't use long polling or web sockets. Instead, I rely on repeated client requests for updates, which adds some latency, but hopefully not too much.
Requirements for graph:
subtrees can be expanded or collapsed
sort nodes with the older siblings above newer siblings
Let's get this figured out!