fix: do template substition after parsing prompt YAML

[dsanders11]

Fixes #117.

[Copilot]

Pull Request Overview

This PR fixes issue #117 by changing when template variable substitution occurs in the prompt file loading process. Instead of replacing template variables in the raw YAML file content before parsing, the substitution now happens after parsing, specifically on the message content fields. This allows template variables to be used within YAML string values without interfering with YAML parsing.

Key changes:

• Template variable substitution moved from pre-parsing to post-parsing stage
• Substitution now applied individually to each message's content field after YAML parsing

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