chore: update repo to use ic-agent 0.45 and resolve conflicts from cargo update

[shilingwang]

Summary

This PR fixes all compilation errors introduced by running cargo update, which updated several dependencies to newer versions with breaking API changes.

Changes

1. proptest (pinned to =1.6.0)

• Issue: proptest 1.10.0 uses rand 0.9.x, incompatible with our rand_chacha 0.3.1 (which uses rand 0.8.x)
• Fix: Pinned proptest to exactly version 1.6.0 in workspace Cargo.toml

2. slog (deprecated macro)

• Issue: slog_o! macro deprecated in favor of slog::o!()
• Fixed in: 2 files (state_tool/commands.rs, embedders/bin/instrument_wasm.rs)

3. assert_cmd (deprecated API)

• Issue: Command::cargo_bin() deprecated in favor of cargo_bin_cmd! macro
• Fixed in: 2 files (fstrim_tool tests, replica tests)

4. ic-agent (v0.40.1 → v0.45.0)

• BasicIdentity::from_pem() now requires bytes directly, not file handles or cursors (4 files)
• AgentError::TransportError now wraps TransportError::Reqwest(e) (1 file)
• HttpService trait signature changed: added size_limit parameter and changed types to http::Request<Bytes> (1 file)

5. wirm (v2.1.0 → v2.2.0)

• Instructions::new() now requires 3 parameters: vec with offset tuples, locals_start, save_offsets (2 files, 4 occurrences)
• Module::parse() now requires 3 parameters, added with_offsets: bool (6 files, 9 occurrences)

6. nix (v0.29.0)

• Issue: Pid and kill now require feature flags
• Fix: Added features = ["process", "signal"] to pocket_ic_server/Cargo.toml

7. ic-utils (v0.40.1 → v0.45.0)

• InstallMode deprecated → use CanisterInstallMode (2 files)
• CanisterStatus deprecated → use CanisterStatusType (1 file)
• take_canister_snapshot() signature changed, requires public crate types (1 file)

8. Missing dependencies

• Added bytes and http to boundary_nodes tests Cargo.toml
• Added ic-management-canister-types to consensus upgrade tests

9. Version conflicts

• Fixed: nns-system-tests had ic-utils = "0.40.1" pinned → changed to { workspace = true }

Test Plan

All changes fix compilation errors. The code should build successfully after these changes.

Files Changed

Total: 28 files modified

• 3 Cargo.toml files (dependencies)
• 1 Cargo.lock (updated)
• 24 source files (API adaptations)

[github-actions]

This pull request changes code owned by the Governance team. Therefore, make sure that
you have considered the following (for Governance-owned code):

1. Update unreleased_changelog.md (if there are behavior changes, even if they are
   non-breaking).

2. Are there BREAKING changes?

3. Is a data migration needed?

4. Security review?

How to Satisfy This Automatic Review

1. Go to the bottom of the pull request page.

2. Look for where it says this bot is requesting changes.

3. Click the three dots to the right.

4. Select "Dismiss review".

5. In the text entry box, respond to each of the numbered items in the previous
   section, declare one of the following:

• Done.

• $REASON_WHY_NO_NEED. E.g. for unreleased_changelog.md, "No
  canister behavior changes.", or for item 2, "Existing APIs
  behave as before.".

Brief Guide to "Externally Visible" Changes

"Externally visible behavior change" is very often due to some NEW canister API.

Changes to EXISTING APIs are more likely to be "breaking".

If these changes are breaking, make sure that clients know how to migrate, how to
maintain their continuity of operations.

If your changes are behind a feature flag, then, do NOT add entrie(s) to
unreleased_changelog.md in this PR! But rather, add entrie(s) later, in the PR
that enables these changes in production.

Reference(s)

For a more comprehensive checklist, see here.

GOVERNANCE_CHECKLIST_REMINDER_DEDUP