Reproduction

First install all dependencies - assumes node and meta are installed globally

npm i
meta npm install

The problem:

1. meta npm run lint

does this:

/private/tmp/trial/meta-bug-16:
npm ERR! missing script: lint

npm ERR! A complete log of this run can be found in:
npm ERR!     /Users/sramam/.npm/_logs/2019-08-30T16_03_25_546Z-debug.log
/private/tmp/trial/meta-bug-16: command 'npm run lint' exited with error: Error: Command failed: npm run lint

repos/node-starter:

> @tufan/node-starter@1.0.0 lint /private/tmp/trial/meta-bug-16/repos/node-starter
> tslint -c tslint.json --project ./tsconfig.json --format stylish

no-use-before-declare is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
no-unused-variable is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
repos/node-starter ✓
 sramam  tmp  trial  meta-bug-16  master

2. meta npm run lint --exclude .

does this:

/private/tmp/trial/meta-bug-16:
npm ERR! missing script: lint

npm ERR! A complete log of this run can be found in:
npm ERR!     /Users/sramam/.npm/_logs/2019-08-30T16_03_35_898Z-debug.log
/private/tmp/trial/meta-bug-16: command 'npm run lint' exited with error: Error: Command failed: npm run lint

repos/node-starter:

> @tufan/node-starter@1.0.0 lint /private/tmp/trial/meta-bug-16/repos/node-starter
> tslint -c tslint.json --project ./tsconfig.json --format stylish

no-use-before-declare is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
no-unused-variable is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
repos/node-starter ✓

$ pwd
/tmp/trial/meta-bug-16

3. meta npm run lint --exclude /tmp/trial/meta-bug-16

does this:

/private/tmp/trial/meta-bug-16:
npm ERR! missing script: lint

npm ERR! A complete log of this run can be found in:
npm ERR!     /Users/sramam/.npm/_logs/2019-08-30T16_03_45_928Z-debug.log
/private/tmp/trial/meta-bug-16: command 'npm run lint' exited with error: Error: Command failed: npm run lint

repos/node-starter:

> @tufan/node-starter@1.0.0 lint /private/tmp/trial/meta-bug-16/repos/node-starter
> tslint -c tslint.json --project ./tsconfig.json --format stylish

no-use-before-declare is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
no-unused-variable is deprecated. Since TypeScript 2.9. Please use the built-in compiler checks instead.
repos/node-starter ✓