Deploying requires inexistent packages

This is a Bug Report

Description

• What went wrong?
  I was developing with serverless-appsync-plugin along with a few lambda, after a few runs of sls deploy it suddenly prompts for missing modules in the node_modules/.bin directory.

  First it wants node-gyp, I manually installed that as a workaround, it then asks for node-ninja. I suspect there is a list of missing internal dependencies from serverless-cli because of some misconfiguration I made in the way.

  I recently updated serverless with sudo npm up -g serverless, not sure if that introduces the error.

• What did you expect should have happened?
  My application should deploy normally like before.

• What was the config you used?

  # Welcome to serverless. Read the docs
  # https://serverless.com/framework/docs/
  
  # Serverless.yml is the configuration the CLI
  # uses to deploy your code to your provider of choice
  # https://serverless.com/framework/docs/providers/aws/guide/serverless.yml/#serverlessyml-reference
  
  # The `service` block is the name of the service
  service: test-api
  
  # The `provider` block defines where your service will be deployed
  provider:
    name: aws
    runtime: nodejs10.x
    stackName: test-api
    deployementPrefix: test
    tracing:
      lambda: true
  
  plugins:
    - serverless-plugin-typescript
  
  functions:
    test:
      handler: lambda/test.handler
      description: Test function that dumps it's input.
  

• What stacktrace or error message from your provider did you see?

  Error: ENOENT: no such file or directory, open '/Users/[REDACTED]/.build/node_modules/.bin/node-ninja'
      at Package.getFileContent (/usr/local/lib/node_modules/serverless/lib/plugins/package/lib/zipService.js:130:15)
      at Package.getFileContentAndStat (/usr/local/lib/node_modules/serverless/lib/plugins/package/lib/zipService.js:119:12)
      at Array.map (<anonymous>)
      at WriteStream.output.on (/usr/local/lib/node_modules/serverless/lib/plugins/package/lib/zipService.js:91:29)
      at WriteStream.emit (events.js:189:13)
      at WriteStream.EventEmitter.emit (domain.js:441:20)
      at /usr/local/lib/node_modules/serverless/node_modules/graceful-fs/graceful-fs.js:231:14
      at /usr/local/lib/node_modules/serverless/node_modules/graceful-fs/graceful-fs.js:258:16
      at FSReqWrap.args [as oncomplete] (fs.js:140:20)
  

Additional Data

• Serverless Framework Version you're using: 1.43.0
• Operating System: darwin
• Stack Trace:
• Provider Error messages: ENOENT: no such file or directory, open '/Users/Vicary/[REDACTED]/.build/node_modules/.bin/node-gyp'

Start with serverless/lib/plugins/package/lib/zipService.js, especially the paths around lines 91-130 shown in the stack trace, and reproduce the deployment using the supplied serverless.yml and Serverless Framework 1.43.0 configuration. Trace why node_modules/.bin/node-gyp or node-ninja is included in the package file list but missing from .build. Done means the deployment no longer fails with the reported ENOENT error.