chore: Bump messenger and controller dependencies

[FrederikBolding]

Replacement for Dependabot PRs as more than one dependency needed to be bumped to get passing CI.

Bumps messenger, base-controller, storage-service, permission-controller & approval-controller.

---

Note

Medium Risk
Upgrades @metamask/messenger to 1.0.0 and bumps several core controller dependencies, which can subtly affect controller messaging/type contracts across Snaps runtime components. Code changes are mostly type-level, but they touch central controllers (SnapController, routing, UI) so integration/CI coverage is important.

Overview
Updates Snaps packages to newer controller/messenger releases (notably @metamask/messenger@1.0.0, plus approval-controller, base-controller, permission-controller@12.3.0, and storage-service).

Refactors Snaps controllers to match updated permission-controller action typings by replacing legacy types (e.g., GetPermissions, HasPermission, UpdateCaveat) with the new PermissionController*Action type exports in SnapController, CronjobController, SnapInsightsController, SnapInterfaceController, and MultichainRoutingService.

Adjusts the simulation setup to align with the updated permission-controller generics by simplifying PermissionController typing and pruning now-unneeded constraint type imports, and updates yarn.lock accordingly.

^{Written by Cursor Bugbot for commit 24da3f4. This will update automatically on new commits. Configure here.}

[socket-security]

Review the following changes in direct dependencies. Learn more about Socket for GitHub.

Diff	Package	Supply Chain Security	Vulnerability	Quality	Maintenance	License
	@​metamask/​base-controller@​9.0.0 ⏵ 9.0.1	+1			+6
	@​metamask/​approval-controller@​9.0.0 ⏵ 9.0.1				+2
	@​metamask/​messenger@​0.3.0 ⏵ 1.0.0			+1	+6
	@​metamask/​permission-controller@​12.2.1 ⏵ 12.3.0			+1	+2
	@​metamask/​storage-service@​1.0.0 ⏵ 1.0.1				+2

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.56%. Comparing base (1d0d356) to head (24da3f4).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3930   +/-   ##
=======================================
  Coverage   98.56%   98.56%           
=======================================
  Files         426      426           
  Lines       12316    12316           
  Branches     1935     1935           
=======================================
  Hits        12139    12139           
  Misses        177      177           

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