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isShopifyLiquidJson matched every templates/**/*.json and sections/**/*.json by path alone, so a .NET project template's template.json (jasontaylordev/ CleanArchitecture), schematics and CMS content were indexed as empty Liquid files, and JSON listing `sections` could link to an unrelated Liquid file. The rule now needs the directory holding templates/ or sections/ to also hold layout/theme.liquid or config/settings_schema.json, looked up under the project root. isSourceFile, detectLanguage and preloadLanguagesForFiles take an optional rootDir, and every caller that decides what to index or how to parse passes it: the scans, git change detection, scoped sync, the watcher, indexAll, indexFileWithContent and CodeGraph.extractFromSource. Without a root there is no theme to find. A sync removes JSON an older index stored this way. Shopify/dawn, expressjs/express and gofynd/Astra index byte-identically; CleanArchitecture loses its 2 bogus Liquid files. Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>