refactor(storage,query): decompose storage & AST god classes, decouple CoreseIO, and purge legacy dead code - #652

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/cache@v4, actions/checkout@v4, actions/setup-java@v4, madrapps/jacoco-report@v1.7.0. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/