fix: refactor amplify.json file handling

[attilah]

Description of changes:

• Together with feature flags amplify.json file introduced in the root folder of the project. It turned out to be a too common name as multiple Amplify projects are involved so to reduce the clutter the file has been renamed to cli.json and cli.{envName}.json accordingly and with this PR it gets created inside the amplify folder.
• push/pull and env add support added to feature flags to cover more scenarios.
• e2e tests covering the above operations also the removal of amplify.json files.

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

[codecov]

Codecov Report

Merging #5282 into master will increase coverage by 0.12%.
The diff coverage is 86.76%.

@@            Coverage Diff             @@
##           master    #5282      +/-   ##
==========================================
+ Coverage   59.75%   59.87%   +0.12%     
==========================================
  Files         392      391       -1     
  Lines       17442    17465      +23     
  Branches     3465     3470       +5     
==========================================
+ Hits        10423    10458      +35     
+ Misses       6397     6384      -13     
- Partials      622      623       +1     

Impacted Files	Coverage Δ
...amplify-cli-core/src/feature-flags/featureFlags.ts	80.48% <81.25%> (-1.24%)	⬇️
...-core/src/feature-flags/featureFlagFileProvider.ts	96.29% <100.00%> (-0.77%)	⬇️
.../amplify-cli-core/src/state-manager/pathManager.ts	70.42% <100.00%> (+25.64%)	⬆️
...amplify-cli-core/src/state-manager/stateManager.ts	50.00% <100.00%> (+9.15%)	⬆️

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[lgtm-com]

This pull request introduces 3 alerts when merging b9d2fe1 into 59734ac - view on LGTM.com

new alerts:

• 3 for Unused variable, import, function or class

[github-actions]

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