Resolve Compiler Warnings for the SIST 1.0.0 Release

[harryswift01]

Summary

Resolve compiler warnings identified while preparing SIST for the 1.0.0 release.

The changes remove uninitialised state and clarify ambiguous control flow while keeping the existing scientific behaviour as close as possible to the current implementation.

Changes

Initialisation fixes:

• Avoid using uninitialised MinWindowSize and MaxWindowSize values in the constructors.
• Initialise profile matrix pointers using the fixed MaxInitialWindowSize bounds.

Cruciform record validation:

• Initialise cruciform record values before use.
• Only store complete and valid cruciform energy records.
• Prevent malformed records from accessing invalid sequence positions.

Compiler warning cleanup:

• Resolve misleading-indentation warnings in trans_three and trans_compete.
• Make existing control flow explicit without intentionally changing behaviour.

Impact

• Both trans_three and trans_compete build cleanly
• Removes identified uninitialised-state and ambiguous-control-flow warnings.
• No intentional changes to scientific parameters, defaults, or supported calculations.

[jimboid]

Looks mostly like indentation fixes etc resulting in cleaner src. The only really relevant change is the maxwindow change. If the tests are still giving correct answers then safe to merge.