Move trans_three and trans_compete C++ sources into a src/ folder

[harryswift01]

Summary

This PR noves the C++ source directories (trans_three/, trans_compete/) into a new src/ folder to give the repo a clearer structure ahead of adding the Python sist package and a shared header. This is a structural change only, no behaviour change.

Changes

Move C++ source directories into src/:

• Relocated trans_three/ → src/trans_three/ and trans_compete/ → src/trans_compete/

Update references to the new source layout:

• Updated CMakeLists.txt include directories and source file lists to point at src/trans_three and src/trans_compete
• Updated master.pl to resolve the compiled qsidd executables via $RealBin/src/trans_three/qsidd and $RealBin/src/trans_compete/qsidd
• Updated tests/conftest.py to build and locate the executables under src/trans_three / src/trans_compete
• Updated .gitignore build-artifact entries (qsidd, depend) to the new src/ paths
• Updated docs (docs/source/installation.rst, docs/source/development.rst, docs/source/source-usage.rst) to reference the new src/ paths in build and usage instructions

Impact

• No user-facing or behavioural change, this is a pure reorganisation of files and their references
• Clears the way for the new sist Python package to live alongside the existing C++ code
• Verified via conda build conda-recipe --override-channels -c conda-forge -c bioconda: all 16 tests pass

[jimboid]

Nicely restructuring in preparation for bringing in the complexity of a python interface. Tests are known to pass for both regression and the conda dry runs which prove the code still builds and there are no missed make strings anywhere. Please merge.