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You can double check that the expected json files were extracted by looking in json-db/src.zip. You can tweak what is extracted by passing --include=<pattern> or --include=!<negated pattern> to the database index-files command.
Beware, that this data cannot be put in the same database that is used for java analysis, and must be a separate database. Then, you can use any CodeQL language library pack that understands YAML to write queries on these files. Currently the library packs that include YAML support are codeql/python-all, codeql/javascript-all and codeql/actions-all. You can then work with the JSON trees importing respectively semmle.python.Yaml, semmle.javascript.YAML or codeql.actions.ast.internal.Yaml.
I have a Java project and its permission settings use JSON file to config. Now I can not use CodeQL to parse JSON file and find BAC issues.
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