Introduce MizerRate S3 class for rate function outputs

[gustavdelius]

Summary

• Introduces the MizerRate S3 class, a lightweight wrapper around species × size matrices returned by rate functions (getEncounter(), getFeedingLevel(), getMort(), getEGrowth(), getFMort(), etc.). It carries rate_name and units attributes and provides enhanced print(), summary(), plot(), and as.data.frame() methods while behaving transparently as a plain matrix for arithmetic and subsetting.
• Centralises dimnames assignment for MizerRate objects inside the constructor.
• Updates all @return tags for get* rate functions in R/rate_functions.R to reflect that they now return a MizerRate object.
• Adds MizerRate and is.MizerRate to the Classes section of the pkgdown reference index.
• Adds a ## The MizerRate class section to vignettes/developer_vignette.Rmd.
• Adds a ## Plotting rate functions section to vignettes/plotting.Rmd demonstrating plot() and as.data.frame() on MizerRate objects.
• Fixes two test failures in tests/testthat/test-project_methods.R caused by MizerRate attribute propagation.

Test plan

• devtools::test() passes with no failures
• devtools::check() passes with no errors or warnings
• devtools::document() regenerates man pages cleanly
• plot(getEncounter(NS_params), NS_params) produces a correctly coloured line plot
• summary(getFeedingLevel(NS_params)) prints a per-species table

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