Describe the bug

When using the analyze tool in the Developer extension, the analysis results cache keys on (path, modified_time) but does not include the analysis mode, causing an order-dependent bug: when directory analysis runs before focused analysis in the same session, the cached Structure-mode data is incorrectly returned for subsequent Semantic-mode requests, resulting in incomplete results bc of missing call chains and references.

To Reproduce
Steps to reproduce the behavior:

1. Start a fresh Goose session with the Developer extension
2. Prompt the model to analyze the current directory in Structure mode (default mode for directories)
   • This caches all files with Structure mode data (basic counts only, no calls/references)
3. Then prompt the model to run focused analysis on any arbitrary symbol you know exists in those files in the codebase

Expected behavior
Focused analysis of the symbol should show incoming/outgoing call chains and detailed references.

Instead, the focused analysis will return missing or incomplete call chains and references for the given symbol.

Please provide following information:

• OS & Arch: Darwin (Sequoia 15.6.1) arm64
• Interface: CLI
• Version: unreleased, built off latest main
• Extensions enabled: computercontroller, developer
• Provider & Model: Databricks + Claude Sonnet 4