This reproduces a Knip v6 path-resolution mismatch when the CLI is pointed at a non-default tsconfig file.

• tsconfig.json has no compilerOptions.paths.
• tsconfig.app.json extends tsconfig.json and defines @app/* -> ./src/*.
• knip.ts has no paths.
• src/main.ts imports src/used.ts via @app/used.
• src/unused.ts is truly unused.

When running with --tsConfig tsconfig.app.json, Knip should understand @app/used and report only src/unused.ts.

pnpm install
pnpm knip
pnpm knip:with-paths
pnpm knip:use-tsconfig-files

• pnpm knip reports both src/used.ts and src/unused.ts as unused.
• pnpm knip:with-paths reports only src/unused.ts.
• pnpm knip:use-tsconfig-files reports nothing and exits 0.

This suggests Knip loads tsconfig.app.json for file context, but the module resolver still does not use its compilerOptions.paths unless aliases are also present in Knip config. --use-tsconfig-files is not equivalent: it avoids the false positive, but also masks the true unused file.