Inconsistent context file instruction handling in Amazon Q CLI

Description: When utilizing context files in Amazon Q CLI, there is an inconsistency in how instructions are followed based on how the context is referenced in prompts.

Current Behavior:

When explicitly referencing the context file in the prompt, Amazon Q CLI correctly follows all instructions and executes all required actions, including file system operations using the tool `fs_write`.
However, when using generic prompts without directly referencing the context file, Amazon Q CLI does not consistently follow all instructions from the context file. This particularly affects operations that require file system interactions.

Expected Output Structure:

Section 1: Code analysis and summary
Section 2: Implementation guide with code examples
Section 3: Markdown file generation in the package

Expected Behavior: Amazon Q CLI should consistently follow all instructions defined in the context file, regardless of whether the context file is explicitly referenced in the prompt or not.

Note: Specific conversation examples cannot be shared due to internal company information restrictions.

Impact: This inconsistency affects the reliability of automated workflows and requires users to explicitly reference context files to ensure all instructions are followed properly.