babel . --copy-files incorrectly copy node_modules - babeljs

Question

I have a project structure like the following:
-rw-r--r-- 1 chung2014 staff 2774 Nov 7 19:13 README.md
-rw-r--r-- 1 chung2014 staff 75 Nov 26 23:27 babel.config.js
drwxr-xr-x 588 chung2014 staff 18816 Nov 26 23:01 node_modules
-rw-r--r-- 1 chung2014 staff 781 Nov 26 22:25 nodemon.json
-rw-r--r-- 1 chung2014 staff 377691 Nov 26 22:08 package-lock.json
-rw-r--r-- 1 chung2014 staff 1551 Nov 26 23:27 package.json
-rw-r--r-- 1 chung2014 staff 2941 Nov 26 23:29 server.js
drwxr-xr-x 11 chung2014 staff 352 Nov 26 23:03 src
drwxr-xr-x 5 chung2014 staff 160 Nov 26 21:55 test
if I have all the source code inside the src directory, (e.g put server.js into src as well), I can have a script babel src --out-dir dist/ --copy-files in my package.json to compile the all the source code in src to dist/ directory.
However, due to some restriction, I cannot put my server.js inside src directory. So when I try to have a script babel . --out-dir dist/ --copy-files in my package.json, I let babel incorrectly copy files in node_modules to dist, which is not what I want.
So my question is how I can just only compile and copy files from both server.js and src/ to the destination directory dist/ without copying files in node_modules/?
$ cat babel.config.js
const presets = [
"#babel/preset-env",
];
module.exports = { presets };

Answer 1

New solution available
--no-copy-ignored is a new argument which allows the value of --ignore to be respected when copying files.
Usage
Example:
babel src -d dist --ignore 'src/**/*.spec.js' --copy-files --no-copy-ignored
The spec files are not going to be present on the output directory.
Source: https://github.com/babel/babel/issues/6226#issuecomment-590283042

Answer 2

The only way to do this would be to drop --copy-files and do --ignore node_modules, e.g.
babel . --out-dir dist/ --ignore node_modules
and you'll also want to ignore dist/ and babel.config.js and anything else in the root that might contain JS files.
babel . --out-dir dist/ --ignore node_modules,dist,babel.config.js
Realistically, the better option would be for server.js to just proxy through to dist instead through, so you could do
babel src --out-dir dist/
and move server.js to src/server.js. If having a server.js is 100% necessary, then have it do require("./dist/server");.

Answer 3

create a script like:
require('fs-extra').copy(
process.argv.slice(-2).shift(),
process.argv.slice(-2).pop(),
{ filter: (src,dist)=>{ return (src.match(/\.js|\.jsx|stories|test/)===null)} },
err => { if (err) return console.error (err); console.log ('Copy success!');
});
and append this to your build command
&& ./scripts/--copy-files src dist/commonjs
the gist:
https://gist.github.com/kmrk/bbc52a4d54b407398aff1695e5b710b7