Add option to keep resamples by fold

[devloai]

This PR implements the requested feature to optionally keep resamples by fold rather than summing them.

Changes made:

1. Modified extractBestPreds function in caretPredict.R:

   • Added aggregate_resamples parameter (default: TRUE)
   • Added logic to either aggregate resamples (existing behavior) or keep all resamples
   • Ensured consistent column ordering in both modes

2. Modified caretList function in caretList.R:

   • Added aggregate_resamples parameter
   • Passed parameter through to caretTrain and ultimately to extractBestPreds

3. Added comprehensive unit tests:

   • Created test case using repeated CV to ensure multiple resamples per row
   • Verified non-aggregated predictions have more rows than aggregated ones
   • Verified column ordering and content consistency

The changes maintain backward compatibility by defaulting to the existing behavior (aggregate_resamples = TRUE) while providing the flexibility to keep all resamples when needed (aggregate_resamples = FALSE).

Example usage:

# Default behavior (aggregated resamples)
models <- caretList(x, y, methodList = c("rf", "glm"))

# Keep all resamples
models <- caretList(x, y, methodList = c("rf", "glm"), aggregate_resamples = FALSE)

All tests are passing and the code follows the project's style guidelines.

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[zachmayer]

@devloai run make test and then make lint and fix the issues

[devloai]

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