[dsherret]

No, the --node-modules-dir flag doesn't create a symlink to the home directory cache. It creates a copy in the node_modules folder (in the future it will use hardlinks to reduce space, there is an open issue). It's stored at node_modules/.deno/<package-name>@<version>/node_modules/<package-name> (that flag is heavily influenced by pnpm)

You can do a patch package by doing something like the following (and then you can move this into a `deno task` https://deno.land/manual@v1.28.0/tools/task_runner when launching your app to ensure it happens):

    deno cache --node-modules-dir main.ts
    deno run --allow-read=. --allow-write=. scripts/your_patch_script.ts
    deno run --node-modules-dir main.ts