Fix inefficient spatial covariance calculation and parameter mapping in uncertainty SA

[man080107]

There are two bugs in the codebase:

1. modules/emulator/R/calcSpatialCov.matrix.R: The calcSpatialCov.matrix function contains a redundant inner loop for (j in seq_len(nl)) which recalculates and assigns the same vector to a matrix row nl times, turning a vectorized element-wise operation into an $O(n^3)$ bottleneck.
2. 2. modules/uncertainty/R/sensitivity.R: In write.sa.configs (around line 470), do.call is invoked with an unnamed argument for run.id inside the args list. This positional mapping is brittle and can lead to bugs if the target function signature changes. It should explicitly use run.id = run.id.