Move opt-in builtin skill toggle state to workspace-scoped config

[VellummyilumVinoth]

Description

It resolves: wso2/product-integrator#1740

Opt-in builtin skills (default: false, e.g. Skill Creator) had their enabled/disabled toggle state persisted in the project-level
config file inside the project directory. This caused personal skill preferences to pollute the project's git working tree, risking
accidental commits into shared repositories. The toggle state was also read by merging enabledSkills from both global and project configs, making scope ambiguous.

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[VellummyilumVinoth]

We are closing this PR, it is addressed in #2380