References of removed dependencies are not deleted from Podfile

tns prepare ios で使用される Podfile の生成およびクリーンアップフローから始め、platforms 配下に生成される Podfile に焦点を当てます。issue に記載されたアンインストールとバージョン変更の手順を再現し、その後、削除された node_modules 依存関係への参照が存在しないこと、また preparation で重複または互換性のない pod が報告されなくなったことを確認します。

Environment
Provide version numbers for the following components (information can be retrieved by running tns info in your project folder or by inspecting the package.json of the project):

• CLI: 6.2.0
• Cross-platform modules: 6.2.0
• Android Runtime: 6.2.0
• iOS Runtime:
• Plugin(s):

Describe the bug
When a dependency is uninstalled, its reference is not deleted from Podfile in platforms and that leads to the error when trying to run the application on device.

To Reproduce

1. tns create myApp --js
2. tns prepare ios
3. npm i tns-core-modules@6.1.0
4. tns prepare ios
5. You will see the following log in the output:

[!] CocoaPods could not find compatible versions for pod "MaterialComponents/Tabs":
  In snapshot (Podfile.lock):
    MaterialComponents/Tabs (= 92.4.0, ~> 92.3)

  In Podfile:
    MaterialComponents/Tabs (~> 84.4)

    MaterialComponents/Tabs (~> 92.3)

None of your spec sources contain a spec satisfying the dependencies: `MaterialComponents/Tabs (~> 92.3), MaterialComponents/Tabs (~> 84.4), MaterialComponents/Tabs (= 92.4.0, ~> 92.3)`.

You have either:
 * out-of-date source repos which you can update with `pod repo update` or with `pod install --repo-update`.
 * mistyped the name or version.
 * not added the source repo that hosts the Podspec to your Podfile.

Note: as of CocoaPods 1.0, `pod repo update` does not happen on `pod install` by default.

[!] There are duplicate dependencies on `MaterialComponents/Tabs` in `Podfile`:

- MaterialComponents/Tabs (~> 92.3)
- MaterialComponents/Tabs (~> 84.4)

and the content of Podfile is the following:

use_frameworks!

target "newPodfileIssue" do
# NativeScriptPlatformSection /Users/myuser/Work/nativescript-cli/scratch/newPodfileIssue/node_modules/@nativescript/core/platforms/ios/Podfile with 9.0
platform :ios, '9.0'
# End NativeScriptPlatformSection


# Begin Podfile - /Users/myuser/Work/nativescript-cli/scratch/newPodfileIssue/node_modules/@nativescript/core/platforms/ios/Podfile
# platform :ios, '9.0'
use_frameworks!

pod 'MaterialComponents/Tabs', '~> 92.3'
# End Podfile

# Begin Podfile - /Users/myuser/Work/nativescript-cli/scratch/newPodfileIssue/node_modules/tns-core-modules/platforms/ios/Podfile
# platform :ios, '9.0'
use_frameworks!

pod 'MaterialComponents/Tabs', '~> 84.4'
# End Podfile

Expected behavior

It should work and the reference to /Users/myuser/Work/nativescript-cli/scratch/newPodfileIssue/node_modules/@nativescript/core/platforms/ios/Podfile should be deleted from Podfile.