Fix sourceSets configuration for packages using type-codegen

[haydenbaker]

Description of changes:

• Because the generated code is flat (no src/main/java and src/main/resources), the same source directory was being set
  • This was also explicitly called out in the TODO removed in this PR
  • Some zip implementations will fail to unzip when there are duplicate entries
• Adds a fail duplicate strategy to our module-conventions plugin so this doesn't happen in the future

Before

META-INF/
META-INF/LICENSE
META-INF/MANIFEST.MF
META-INF/NOTICE
META-INF/services/
META-INF/services/software.amazon.smithy.model.traits.TraitService
META-INF/smithy-java/
META-INF/smithy-java/type-mappings.properties
META-INF/smithy-java/type-mappings.properties
META-INF/smithy/
META-INF/smithy/errors.smithy
META-INF/smithy/manifest
META-INF/smithy/trait.smithy
errors.smithy
software/
software/amazon/
software/amazon/smithy/
software/amazon/smithy/framework/
software/amazon/smithy/framework/knowledge/
software/amazon/smithy/framework/knowledge/ImplicitErrorIndex.java
software/amazon/smithy/framework/traits/
software/amazon/smithy/framework/traits/ImplicitErrorsTrait.java
software/amazon/smithy/framework/transform/
software/amazon/smithy/framework/transform/AddFrameworkErrorsTransform.java
software/amazon/smithy/java/
software/amazon/smithy/java/framework/
software/amazon/smithy/java/framework/model/
software/amazon/smithy/java/framework/model/AccessDeniedException.java
software/amazon/smithy/java/framework/model/AccessDeniedException.java
software/amazon/smithy/java/framework/model/InternalFailureException.java
software/amazon/smithy/java/framework/model/InternalFailureException.java
software/amazon/smithy/java/framework/model/MalformedRequestException.java
software/amazon/smithy/java/framework/model/MalformedRequestException.java
software/amazon/smithy/java/framework/model/NotAuthorizedException.java
software/amazon/smithy/java/framework/model/NotAuthorizedException.java
software/amazon/smithy/java/framework/model/Schemas.java
software/amazon/smithy/java/framework/model/Schemas.java
software/amazon/smithy/java/framework/model/SharedSerde.java
software/amazon/smithy/java/framework/model/SharedSerde.java
software/amazon/smithy/java/framework/model/ThrottlingException.java
software/amazon/smithy/java/framework/model/ThrottlingException.java
software/amazon/smithy/java/framework/model/UnknownOperationException.java
software/amazon/smithy/java/framework/model/UnknownOperationException.java
software/amazon/smithy/java/framework/model/ValidationException.java
software/amazon/smithy/java/framework/model/ValidationException.java
software/amazon/smithy/java/framework/model/ValidationExceptionField.java
software/amazon/smithy/java/framework/model/ValidationExceptionField.java
trait.smithy

After

META-INF/
META-INF/LICENSE
META-INF/MANIFEST.MF
META-INF/NOTICE
META-INF/services/
META-INF/services/software.amazon.smithy.model.traits.TraitService
META-INF/smithy-java/
META-INF/smithy-java/type-mappings.properties
META-INF/smithy/
META-INF/smithy/errors.smithy
META-INF/smithy/manifest
META-INF/smithy/trait.smithy
software/
software/amazon/
software/amazon/smithy/
software/amazon/smithy/framework/
software/amazon/smithy/framework/knowledge/
software/amazon/smithy/framework/knowledge/ImplicitErrorIndex.java
software/amazon/smithy/framework/traits/
software/amazon/smithy/framework/traits/ImplicitErrorsTrait.java
software/amazon/smithy/framework/transform/
software/amazon/smithy/framework/transform/AddFrameworkErrorsTransform.java
software/amazon/smithy/java/
software/amazon/smithy/java/framework/
software/amazon/smithy/java/framework/model/
software/amazon/smithy/java/framework/model/AccessDeniedException.java
software/amazon/smithy/java/framework/model/InternalFailureException.java
software/amazon/smithy/java/framework/model/MalformedRequestException.java
software/amazon/smithy/java/framework/model/NotAuthorizedException.java
software/amazon/smithy/java/framework/model/Schemas.java
software/amazon/smithy/java/framework/model/SharedSerde.java
software/amazon/smithy/java/framework/model/ThrottlingException.java
software/amazon/smithy/java/framework/model/UnknownOperationException.java
software/amazon/smithy/java/framework/model/ValidationException.java
software/amazon/smithy/java/framework/model/ValidationExceptionField.java

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