refactor(snaps-rpc-methods)!: Use messenger for permitted methods

[FrederikBolding]

Migrate the permitted method handlers to use the messenger where applicable.

https://consensyssoftware.atlassian.net/browse/WPC-995

---

Note

Medium Risk
Refactors many permitted RPC handlers to route through controller messenger.call actions instead of direct hook functions, which can subtly change permission checks, origin handling, and side effects across core Snap RPC methods.

Overview
Permitted Snap RPC methods are migrated from hook-based implementations to messenger-driven controller actions. Handlers now declare actionNames, accept JsonRpcRequestWithOrigin, and call into actions like PermissionController:hasPermission, SnapController:*, CronjobController:*, WebSocketService:*, KeyringController:getState, and SnapInterfaceController:*.

This removes the exported permitted handlers list and updates schema generation to read permitted methods from src/permitted/middleware.ts instead of the deleted handlers.ts, with associated test updates to use MockControllerMessenger and origin middleware.

Also tightens the get-file example by asserting snap_getFile returns content before JSON.parse, updates its manifest shasum, and adjusts Jest coverage thresholds slightly.

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[FrederikBolding]

Turns out the types here have always been wrong

[FrederikBolding]

This has always been possible, but the type was wrong.

[FrederikBolding]

TypeScript failed to generate declarations for this, but we don't actually need to export it, so I moved it here and stopped exporting.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.58%. Comparing base (92ace80) to head (399e36b).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3987   +/-   ##
=======================================
  Coverage   98.58%   98.58%           
=======================================
  Files         427      425    -2     
  Lines       12408    12368   -40     
  Branches     1949     1949           
=======================================
- Hits        12232    12193   -39     
+ Misses        176      175    -1     

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[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

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[FrederikBolding]

Some of the tests were not correctly nested under the describe() which results in some whitespace changes. Likely easier to review with whitespace off.