Bugfix: Ensure CLI Var files have highest precedence

[yorinasub17]

Description

Fixes https://github.com/gruntwork-io/boilerplate/issues/117

This fixes a bug in boilerplate where the variable definitions passed in the CLI did not have the highest precedence, being overwritten by the variable definitions on the Dependency.

TODOs

Read the Gruntwork contribution guidelines.

• [x] Update the docs.
• [x] Run the relevant tests successfully, including pre-commit checks.
• [x] Ensure any 3rd party code adheres with our license policy or delete this line if its not applicable.
• [x] Include release notes. If this PR is backward incompatible, include a migration guide.

Release Notes (draft)

• Fixed bug where the variable definitions passed in the CLI did not have the highest precedence, being overwritten by the variable definitions on the Dependency.

[yorinasub17]

Thanks for review! Merging now.