fix(cli): Update warp apply to apply changes in single command

[ltyu]

Description

This PR fixes a limitation in warp apply such that it can only extend or update an existing warp route. This means that for configs with both changes require warp apply to be called multiple times. An example is when Renzo deploys to new chain, and it needs to update the existing ISMs.

Related issues

• Fixes fix: warp apply requires multiple calls for multiple updates #4671

Backward compatibility

Yes

Testing

Manual/Unit Tests

[changeset-bot]

🦋 Changeset detected

Latest commit: e4be6d8

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 9 packages

Name	Type
@hyperlane-xyz/cli	Minor
@hyperlane-xyz/ccip-server	Minor
@hyperlane-xyz/github-proxy	Minor
@hyperlane-xyz/helloworld	Minor
@hyperlane-xyz/infra	Minor
@hyperlane-xyz/sdk	Minor
@hyperlane-xyz/utils	Minor
@hyperlane-xyz/widgets	Minor
@hyperlane-xyz/core	Patch

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[yorhodes]

mostly lgtm although it would intuitively make more sense to me if we did

contracts = contracts.extend()
contracts.update()

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.85%. Comparing base (adedb3d) to head (e4be6d8).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4672   +/-   ##
=======================================
  Coverage   73.85%   73.85%           
=======================================
  Files         100      100           
  Lines        1423     1423           
  Branches      181      181           
=======================================
  Hits         1051     1051           
  Misses        351      351           
  Partials       21       21           

Components	Coverage Δ
core	84.61% <ø> (ø)
hooks	75.71% <ø> (ø)
isms	78.94% <ø> (ø)
token	88.23% <ø> (ø)
middlewares	77.39% <ø> (ø)