[Feature]: Move C++ source into a `src/` folder

[harryswift01]

Feature Request

Problem / Motivation

Everything currently sits loose at the repo root (trans_three/, trans_compete/, master.pl, etc). We're about to add a Python package and a shared C++ header, and there's nowhere sensible to put them without a proper src/ layout.

Proposed Solution

Move trans_three/ and trans_compete/ into src/, and fix up the paths that point at them (build scripts, conda recipe, tests, master.pl). No behaviour change just moving files

Expected Impact

• No user-facing change
• Clears the way for the new sist package to live alongside the C++ code