Anchor the working and data directories to the installation

Both defaulted to the current directory, and the server is normally started
through a workspace filter — so it ran with its own package as the working
directory. Room data would have landed in apps/server/data, and the agent
would have defaulted to reading the server's own source rather than the
project it was meant to be planning against.

Both now default to the repository root, derived from this file rather than
from however the process happened to be launched.