refactor: `DatabaseGroundedFDRControl.fit` mutates its input DataFrame

## Summary

`DatabaseGroundedFDRControl.fit` (`winnow/fdr/database_grounded.py`) changes the
DataFrame you pass in. A `fit` should really leave its input alone. This was raised in
a review but unrelated to the current PR, so tracking it here.

## Description & Purpose

Right now `fit` writes straight back into the caller's DataFrame: it overwrites
`sequence` and `prediction`, and adds `num_matches` and `correct`. Two issues
with that:

- Those side effects are easy to miss, since nothing about `fit` hints the input
will change.
- If someone passes a slice, the writes hit a copy, pandas raises
`SettingWithCopyWarning`, and the method silently fails.

Proposed fixes, roughly in order of preference:

1. Take what we actually need instead of a whole DataFrame: `sequence`,
`prediction`, and confidence. Cleaner contract, no column-layout coupling.
2. If we keep the DataFrame, copy it first (`dataset = dataset.copy()`) and work
on the copy. Return it if callers want the `num_matches` / `correct` columns.
3. Either way, fix the docstring and possibly also the function the name to match what it does,
e.g. `estimate`, `calibrate`, or `add_calibration_columns`. Note `fit` is part of
the `FDRControl` base interface (`winnow/fdr/base.py`), so a rename touches
`NonParametricFDRControl` and the call sites too.

Worth noting `NonParametricFDRControl.fit` already sidesteps this by working on
arrays via `.to_numpy()`, so option 1 would line the two up.

## Additional Notes

- Check `tests/fdr/` and call sites before changing the signature or name, and
make sure nothing downstream relies on the mutated columns.

### Description & Purpose:

_No response_

### Additional Notes:

_No response_

Start in winnow/fdr/database_grounded.py and compare DatabaseGroundedFDRControl.fit with NonParametricFDRControl.fit, then inspect the FDRControl interface in winnow/fdr/base.py. Search tests/fdr/ and call sites for reliance on mutated columns or the current signature before choosing an approach. Done means fit no longer mutates caller-owned input, its contract and docstring are consistent, and the relevant tests pass.

Written by the indexing model from the issue text.