fix: Fix merge for multiresourceyaml resources (#122)

[Ruari-Phipps]

Summary

Fix incorrect merge behaviour for MultiResourceYamlResource types by performing the 3-way merge at the file level rather than per-resource.

Motivation

MultiResourceYamlResource types (e.g. entities) store multiple resources in a single YAML file. The previous code performed the 3-way merge per-resource and then wrote each resource individually, which meant the common ancestor used for the merge was wrong and resources from the same file would overwrite each other.
It would also crash.

Changes

• Before the merge loop, serialise the original resources into a file-level cache to use as the common ancestor
• Skip the per-resource string merge for MultiResourceYamlResource types during the main loop; instead accumulate them into the cache
• After the main loop, perform the 3-way merge at the file level and write the result
• Gate write_cache_to_file behind force mode, since non-force mode now handles writing via the file-level merge loop

Test strategy

• Added/updated unit tests
• Manual CLI testing (poly pull)
• Tested against a live Agent Studio project
• N/A (docs, config, or trivial change)

Checklist

• ruff check . and ruff format --check . pass
• pytest passes
• No breaking changes to the poly CLI interface (or migration path documented)
• Commit messages follow conventional commits
• ## Screenshots / Logs