Update the fastly.toml manifest if missing manifest_version.

[Integralist]

Problem: the error message (see below) was being shown every time fastly compute build was executed. This happened because although the logic set a correct manifest_version value, that only happened in-memory and so the same error would happen each time the CLI was used (unless the user manually updated the file).

The fastly.toml was missing a `manifest_version` field. A default schema version of `1` will be used.

Additionally to this I discovered that the current implementation wouldn't write the manifest_version to the file correctly. It would be written as a separate block [manifest_version] rather than as a top-level field. So I've refactored the logic to fix that bug.

[kailan]

Got a weird dynamic config related error but I don't think it's anything to do with these changes.

kailan@KB-Fastly not-real-cli-config % ../../fastly/cli/fastly compute build

WARNING: The fastly.toml was missing a `manifest_version` field. A default schema version of `1` will be used.

✓ Initializing...
✓ Verifying package manifest...
- Checking if Rust 1.49.0 is installed...
ERROR: Get "https://developer.fastly.com/api/internal/cli-config": context deadline exceeded.

This error may be caused by transient network issues. Please verify your network connection and try again.

kailan@KB-Fastly not-real-cli-config % ../../fastly/cli/fastly compute build
✓ Initializing...
✓ Verifying package manifest...
✓ Verifying local rust toolchain...
✓ Building package using rust toolchain...
✓ Creating package archive...

SUCCESS: Built rust package cli-config (pkg/cli-config.tar.gz)

The manifest_version functionality works as intended. Test case looks good. Ship it 🚀