rootDir & outDir have to be explicitly set

[ericclemmons]

Without rootDir

It keeps the nesting of src under dist

+ dist
+   package.json
+   src/
+     index.js
  src/
    index.ts

With rootDir: "./src"

It generates files within ./src

  src/
+   index.js  
    index.ts
-   package.json
+   package.json

With rootDir: "./src" & outDir: "./dist"

Fixes the dist/src nesting and generates the output as expected.

+ diff
+  index.js
  src/
    index.ts
- package.json
+ package.json

[colinhacks]

As with tsc, zshy infers the rootDir to be the common ancestor of your entrypoints. I'm assuming you're listing "./package.json"? Which is causing it to infer the root dir as "." instead of "./src". This is fixed in the linked PR.