[Feature]: Clean repository for the SIST 1.0.0 release

[harryswift01]

Feature Request

Problem / Motivation

The repository currently contains tracked build artefacts and generated files alongside the maintained source.

These should be cleaned up before the SIST 1.0.0 release so that the repository can be rebuilt reliably from source.

Proposed Solution

• Remove tracked cmake-build-debug/ files.
• Remove tracked *.o files.
• Remove tracked trans_three/qsidd and trans_compete/qsidd binaries.
• Review generated files under example/.
• Update .gitignore where required.
• Verify a fresh clone builds successfully.
• Run the regression suite after cleanup.
• Leave irf308.linux.exe unchanged until its dependency status is resolved.

Alternatives Considered

• Keep the existing generated build artefacts.

Expected Impact

• Cleaner maintained source tree.
• Reduced risk of stale build artefacts being used.
• Reproducible builds from a fresh clone.

Additional Context

The regression suite now provides protection against unintended scientific changes during cleanup.