Fix unresolved path variables during ingestion

[tomvothecoder]

Description

When DOUT_S_ROOT in env_run*.xml contains unresolved shell variables ($CIME_OUTPUT_ROOT, $CASE), the simulation detail page displays raw variable names instead of actual paths.

This PR adds a post-parse substitution step in the ingestion pipeline that resolves these variables using values extracted from env_build*.xml (CIME_OUTPUT_ROOT) and env_case*.xml (CASE).

Changes:

• Extract CIME_OUTPUT_ROOT from parse_env_build()

• Add _substitute_path_variables() helper in case_docs.py to replace $VAR and ${VAR} forms

• Wire substitution into _parse_all_files() for archive_path and output_path

• Add unit and integration tests

• Closes [Bug]: Simulation detail page sometimes renders archive path variables unsubstituted #181

Checklist

• Code follows project style guidelines
• Self-reviewed code
• No new warnings
• Tests added or updated (if needed)
• All tests pass (locally and CI/CD)
• Documentation/comments updated (if needed)
• Breaking change noted (if applicable)

Deployment Notes (if any)

No migration or deployment changes needed. Already-ingested simulations with unresolved paths are not retroactively fixed — a re-ingestion would be needed for those.

[chatgpt-codex-connector]

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