fix(semantic): do not materialize missing DAG roots

[ranxi2001]

Description

SemanticDagExecutor._list_dir() treated every listing failure as a valid empty
directory. If a queued semantic root referred to a file removed by chunking, the DAG
therefore continued to sidecar writeback. VikingFS.write_file() created the missing
parent first, turning the old file URI into either an empty directory or a directory
containing only .abstract.md and .overview.md.

This change preserves the listing exception so the existing dispatch error path stops
that node before any sidecar write. A real empty directory still returns an empty list
and receives its normal generated sidecars.

Human Involvement

• A human participated in the implementation or review loop
• This PR was generated entirely by AI agents without human participation in the loop

Related Issue

Fixes #4461

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactoring (no functional changes)
• Performance improvement
• Test update

Changes Made

• stop converting semantic DAG list failures into empty-directory results;
• cover missing and non-directory roots with both successful and failed sidecar writes; and
• verify that valid empty directories still receive generated sidecars.

Testing

• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have tested this on the following platforms:
  • Linux
  • macOS
  • Windows

Local checks:

• 16 relevant semantic DAG, parent propagation, and directory enumeration tests passed;
• Ruff lint passed on both changed files and the new test is formatter-clean;
• Python compile checks and git diff --check passed.

The broader DAG test selection has eight failures on the unmodified base as well: two
tests require a local OpenViking config, and six test doubles do not accept the current
creator_acl_grant keyword. Editable installation is also unavailable here because
Cargo and the generated native openviking/bin/ov artifact are absent, so tests were
run from source using an existing project test environment.

Checklist

• My code follows the project's coding style
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published

Screenshots (if applicable)

Not applicable; this change has no visual output.

Additional Notes

This prevents new phantom directories. It intentionally does not remove existing ones,
because automated cleanup cannot safely distinguish them from user-created directories.