Hello,

Discussion of this issue took place in this Discord thread. @Zamiell summarized it nicely:

yeah i guess something in tstl broke

mkdir test
cd test
npm init --yes
npm install --save typescript typescript-to-lua
mkdir src
echo 'const x = 1;' > src/main.ts
vim tsconfig.json
(paste in config from getting started page)
npx tstl

that results in a main.lua file in root dir instead of in subdir
which im pretty sure is different from historical behavior

It doesn't matter where the file is in the folder hierarchy - it ends up compiling and storing the file in the root directory.

The configuration from the getting started page, at the time of writing, is:

{
  // Optional: Schema file for hints and validation
  "$schema": "https://raw.githubusercontent.com/TypeScriptToLua/TypeScriptToLua/master/tsconfig-schema.json",

  // ... tsconfig options

  "tstl": {
    // Custom options
  }
}