`cre init` overwrites existing project secrets when adding a new workflow

[EmanHerawy]

Description

When running cre init inside an existing CRE project to add a new workflow, the command overwrites the existing project secrets, removing all previously defined secrets from secrets.yaml.

This behavior makes it easy to accidentally lose critical configuration and secrets when extending a project.

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Steps to Reproduce

1. Create a CRE project and define secrets in secrets.yml
2. Run cre init again in the same project to add a new workflow
3. Observe that secrets.yml is overwritten and existing secrets are removed

Environment

• CRE CLI version: cre version v1.0.3