Replace the interim Step adapter with real run() parameters

[mikub97]

The three built-in steps are currently wrapped by an adapter that sets sys.argv and calls the script's own main(). It works and is honest about being interim, but it means:

• tuning still comes from module-level constants rather than ctx.params(), so it cannot vary per study without editing the source;
• the step chdirs into the project directory, because the scripts resolve paths relative to the working directory;
• --window / --step cannot be passed through.

Where

• packages/dims-analysis/dims_analysis/steps/{rqa,crqa,crosswavelet}.py — the block marked Step contract adapter
• Contract: docs/contracts/step.md

What to do

Give run(config, ctx) the real work: move the body of main() into it, take paths from ctx, take tuning from ctx.params(), and delete the argparse block and the adapter. Do one step at a time.

This pairs naturally with #5 (deduplicating the helpers), since both touch the same three files.

Acceptance

• dims-analysis run produces byte-identical output to today for the same input.
• No step calls os.chdir or reads sys.argv.
• {"analysis": {"rqa": {"window": 5.0}}} in config.json changes the window.

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