Standardize plot generic first-argument name to object for biomass/yield APIs

[Copilot]

plotBiomass(), plotYield(), and plotYieldGear() were inconsistent with the rest of the plotting API by naming the S3 dispatch argument sim instead of object. This change aligns those generics (and related methods/wrappers) with package conventions and records the named-argument impact as a breaking change.

• API surface alignment

  • Renamed first parameter sim → object in:
    • plotBiomass(), plotYield(), plotYieldGear() generics
    • plotBiomass.MizerSim(), plotYield.MizerSim(), plotYieldGear.MizerSim()
    • plotlyBiomass(), plotlyYield(), plotlyYieldGear()
  • Updated internal references/defaults in R/plots.R to use object.

• Documentation sync

  • Updated corresponding Rd usage/argument sections:
    • man/plotBiomass.Rd
    • man/plotYield.Rd
    • man/plotYieldGear.Rd

• Breaking-change note

  • Added NEWS entry under Breaking changes documenting that named calls using sim = ... must switch to object = ....

plotYield <- function(object, ...) UseMethod("plotYield")
plotYield.MizerSim <- function(object, sim2, species = NULL, ...) { ... }
plotlyYield <- function(object, sim2, species = NULL, ...) { ... }

[gustavdelius]

Do not add these tests.

[gustavdelius]

@copilot remove the tests you added

[Copilot]

Done in commit 922191d.