Let extensions upgrade their own data via versioned @extensions

[gustavdelius]

Summary

mizer can upgrade its own (core) slots across mizer versions, but extension
packages had no way to migrate their data when their storage layout changes,
and an object carried no record of which extension version it conformed to.
This PR adds per-extension version tracking and an upgrade-dispatch path so an
extension can upgrade its objects independently of the mizer version.

The motivating case is mizerMR moving its resource_params data frame to a new
location; with this PR a saved mizerMR model is migrated automatically the first
time it passes through validParams() / readParams().

What changed

• Versioned @extensions slot. Slot type widened to "ANY". It may hold
  the legacy named character vector of requirement strings, or a named list of
  c(requirement = ..., version = ...) entries, where version is the version
  of the extension package the object conforms to. objectExtensions() returns
  the requirement-only view, so all dispatch / suffix-chain logic is unchanged.
  New helpers: exported recordExtension() plus internal
  extensionRequirements(), extensionVersions(), extensionVersion(),
  makeExtensions().
• upgrade() methods. upgradeParams() / upgradeSim() are now the
  upgrade.MizerParams() / upgrade.MizerSim() methods of the
  utils::upgrade() generic; the old names remain as thin internal wrappers.
  Extensions register their own method with @exportS3Method utils::upgrade.
• Orchestration in validParams(). It runs the core upgrade when
  @mizer_version is stale, then runExtensionUpgrades() calls each
  out-of-date extension's upgrade method directly (no NextMethod()) and
  re-stamps it afterwards. Extension methods are pure, idempotent migrations.
• needs_upgrading() now also fires when an extension's recorded stamp is
  missing or older than the installed package version. A missing stamp counts
  as stale, so objects created before version tracking are migrated and stamped
  on first use.
• registerExtensions(), readParams()/readSim() and
  requiredExtensionPackages() accept the versioned list form.
• New vignette section "Upgrading objects across versions of your extension".

Testing

• New tests/testthat/test-extension-versions.R.
• Full suite green: 2827 tests, 0 failures, 0 errors.

Note: the unrelated getFluxGradient() doc cross-references that document()
would otherwise add were left out to keep this PR focused.

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