fix: remove CONFIG_DIR exclusion from zip stage to preserve dependency agentcore/ packages

[aidandaly24]

Description

PR #844 fixed the flat name-based agentcore exclusion in copySourceTree by threading rootDir through the recursive traversal, so only the project-root agentcore/ config directory is excluded during the copy stage. However, the same CONFIG_DIR exclusion remained in collectFiles/collectFilesSync (the zip stage).

The zip stage operates on the staging directory — not the project root. When uv pip install --target stagingDir installs a dependency that contains a top-level agentcore/ Python package (e.g., langgraph-checkpoint-aws ships langgraph_checkpoint_aws/agentcore/), the check entry.name === CONFIG_DIR && resolve(directory) === resolve(rootDir) fires at the staging root, silently stripping the package from the deployment zip.

Fix: Remove the CONFIG_DIR exclusion from collectFiles and collectFilesSync entirely. The exclusion is only needed in copySourceTree (which copies from the project root into staging and already correctly filters the config dir). By the time we zip, the project config agentcore/ was already excluded — the only agentcore/ in staging is a legitimate dependency package.

Changes:

1. Removed rootDir parameter and CONFIG_DIR check from collectFiles (async)
2. Removed rootDir parameter and CONFIG_DIR check from collectFilesSync
3. Updated callers (createZipFromDir, createZipFromDirSync) to drop the rootDir argument
4. Updated 2 existing zip tests to reflect that the zip stage no longer excludes agentcore/
5. Added 2 new tests simulating the real staging directory scenario where a dependency's agentcore/ subpackage must survive the zip step

Related Issue

Closes #843

Documentation PR

N/A

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update
• Other (please describe):

Testing

How have you tested the change?

• I ran npm run test:unit and npm run test:integ
• I ran npm run typecheck
• I ran npm run lint
• If I modified src/assets/, I ran npm run test:update-snapshots and committed the updated snapshots

Unit tests: 41/41 packaging tests pass (39 existing + 2 new staging-scenario tests).

End-to-end verification:

1. Built and globally installed the patched CLI
2. agentcore create → agentcore add agent (Strands/Python)
3. uv add langgraph-checkpoint-aws (installs v1.0.7 with agentcore/ subpackage)
4. agentcore package → inspected zip: all 11 langgraph_checkpoint_aws/agentcore/* files present
5. agentcore deploy → agentcore invoke → agent responded successfully, no ModuleNotFoundError

Checklist

• I have read the CONTRIBUTING document
• I have added any necessary tests that prove my fix is effective or my feature works
• I have updated the documentation accordingly
• I have added an appropriate example to the documentation to outline the feature, or no new docs are needed
• My changes generate no new warnings
• Any dependent changes have been merged and published

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[agentcore-cli-automation]

LGTM — the change is correct and minimal.

Verified:

• The only callers of createZipFromDir(Sync) are python.ts and node.ts, both passing a staging directory (never the project root).
• copySourceTree already excludes <srcDir>/agentcore/ before the zip stage runs, so the project's config agentcore/ can never end up at the staging root.
• Any top-level agentcore/ present in the staging root can therefore only be a dependency installed by uv pip install --target stagingDir and should be preserved.
• CONFIG_DIR is still used elsewhere in the file, so the import is not orphaned.
• Tests cover both the existing fixture (now asserting the zip preserves top-level agentcore/) and the real staging scenario.

One minor note on the PR description (not blocking): the end-to-end example uses langgraph-checkpoint-aws, whose agentcore/ is nested under langgraph_checkpoint_aws/ rather than sitting at the staging root. Nested agentcore/ directories were already preserved by the post-#844 zip code (the resolve(directory) === resolve(rootDir) guard wouldn't fire for them), so that specific package isn't actually a repro of the remaining bug. The fix is still valid — it closes a real gap for any dependency that would install a top-level agentcore/ package into staging — but the description's framing of which files were being stripped may be worth clarifying in the commit message for future archaeology.

[github-actions]

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