End-to-end integration test for code JSON store + dense index (supersedes #3 once complete)

[paco-barreras]

Description:
Implement a full integration test for building and querying the code JSON store and dense index.

Requirements:

* Use a fixture repo with files:
    * alpha.py
    * beta.py
* The test should:
    * Run both build and build-json commands
    * Validate outcomes using:
        * get_code_context CLI: checks correct retrieval of code elements
        * query_json_context: verifies searching for decorators works
* Note: When complete, this will fully supersede issue #3 (close #3).