References of removed dependencies are not deleted from Podfile

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 * out-of-date source repos which you can update with `pod repo update` or with `pod install --repo-update`.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.

從 tns prepare ios 使用的 Podfile 產生與清理流程開始，重點關注 platforms 下產生的 Podfile。重現 issue 中的解除安裝與版本變更步驟，然後確認已移除的 node_modules 相依項目參照不存在，且準備流程不再回報重複或不相容的 pod。