Refactor: Reorganize repository structure

[sheepdestroyer]

This PR reorganizes the repository structure by moving scripts to scripts/ and python tests to tests/, merging the duplicate memory MCP tests into router/tests/test_memory_mcp.py, and updating all references, CI workflows, and documentation accordingly.

Summary by Sourcery

Reorganize test and script layout into dedicated scripts/ and tests/ directories and merge duplicate memory MCP tests into a single router-focused suite.

Bug Fixes:

• Fix test and helper script imports and paths after moving files into scripts/ and tests/ directories.

Enhancements:

• Document the new locations and roles of scripts, verification tools, and tests in README and scripts/README.
• Consolidate memory MCP test coverage into router/tests/test_memory_mcp.py and remove duplicate root-level tests.
• Update CI workflow, helper scripts, and upgrade plan docs to use the new script and test paths.

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[sourcery-ai]

Reviewer's Guide

Refactors the repo layout by moving shell/Python scripts under scripts/, consolidating memory MCP tests under router/tests, relocating root tests into tests/, and updating imports, docs, and CI workflows to match the new structure.

File-Level Changes

Change	Details	Files
Reorganize documentation to describe the new scripts/ and tests/ layout and list newly documented helper scripts and test files.	Expanded scripts README to include verification/verify_breaker.py and newly added maintenance/helper daemons. Updated classifier section to include host_agy_daemon.py, sync_gemini_token.py, get_pr_status.py, watch_quota.sh, and test_quota_reset.sh. Rewrote integration test suite section to reference tests/ paths and added subsections for simulation, utility, and helper daemon tests. Updated root README tree to show scripts/ and tests/ directories instead of individual files in the repo root. Adjusted usage examples to call tests/test_agy_tiers.py and scripts/host_agy_daemon.py paths.	scripts/README.md README.md
Update CI workflow and scripts to call tests and verification utilities from their new locations under scripts/ and tests/.	Changed pytest invocation in GitHub Actions to ignore tests/test_agy_behavior.py and tests/test_agy_tiers.py instead of root files. Updated CI breaker verification step to run scripts/verification/verify_breaker.py. Updated CI integration verification step to run tests/test_a2_verify.py. Adjusted start-stack.sh to invoke scripts/sync_gemini_token.py instead of the root-level script. Fixed watch_quota.sh to locate test_quota_reset.sh via SCRIPT_DIR and reflect moved script path.	.github/workflows/test.yml start-stack.sh scripts/watch_quota.sh
Move root-level and router memory MCP tests into a single consolidated router/tests/test_memory_mcp.py module and update imports.	Created router/tests/test_memory_mcp.py combining tests from router/test_memory_mcp.py and test_memory_mcp.py. Removed obsolete router/test_memory_mcp.py and test_memory_mcp.py files. Ensured consolidated tests import memory_mcp via PATH injection to router/ and validate key generation, parsing, and value handling for memory MCP functionality.	router/tests/test_memory_mcp.py router/test_memory_mcp.py test_memory_mcp.py
Relocate root-level integration and helper tests into tests/ and fix their import paths to match the new directory structure.	Moved test_host_agy_daemon.py to tests/test_host_agy_daemon.py and updated sys.path to import host_agy_daemon from scripts/. Moved test_sync_gemini_token.py to tests/test_sync_gemini_token.py and adjusted sys.path to point at the scripts/ directory. Moved test_a2_verify.py, test_circuit_breaker.py, test_models_proxy.py to tests/ equivalents and updated sys.path insertions to import from router/ via parent.parent. Added sys.path insertion in router/tests/test_agy_proxy.py to include the router/ parent for imports. Updated triage_upgrade_plan.md to refer to tests/test_agy_tiers.py and tests/test_classifier_accuracy.py instead of root files.	tests/test_host_agy_daemon.py tests/test_sync_gemini_token.py tests/test_a2_verify.py tests/test_circuit_breaker.py tests/test_models_proxy.py router/tests/test_agy_proxy.py triage_upgrade_plan.md

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[sourcery-ai]

Hey - I've left some high level feedback:

• Several tests now manipulate sys.path manually to reach router and scripts modules; consider turning router and scripts into proper packages or using relative imports to avoid ad‑hoc path injection and make imports more robust.
• The long sys.path parent traversals (e.g., in scripts/verification/verify_breaker.py) are a bit brittle; encapsulating this in a helper or using a consistent project root discovery mechanism would reduce duplication and future breakage if the layout changes again.
• Since start-stack.sh now calls scripts/sync_gemini_token.py, it might be worth adding a simple check that the script exists or fails fast with a clear message if the repository structure is not as expected.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- Several tests now manipulate sys.path manually to reach router and scripts modules; consider turning router and scripts into proper packages or using relative imports to avoid ad‑hoc path injection and make imports more robust.
- The long sys.path parent traversals (e.g., in scripts/verification/verify_breaker.py) are a bit brittle; encapsulating this in a helper or using a consistent project root discovery mechanism would reduce duplication and future breakage if the layout changes again.
- Since start-stack.sh now calls scripts/sync_gemini_token.py, it might be worth adding a simple check that the script exists or fails fast with a clear message if the repository structure is not as expected.

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: f1953398-9cb5-43af-b740-a7f8c1e97416

📥 Commits

Reviewing files that changed from the base of the PR and between 778da4d and cad53cb.

📒 Files selected for processing (32)

• .github/workflows/test.yml
• README.md
• router/test_memory_mcp.py
• router/tests/test_agy_proxy.py
• router/tests/test_memory_mcp.py
• scripts/README.md
• scripts/get_pr_status.py
• scripts/host_agy_daemon.py
• scripts/sync_gemini_token.py
• scripts/test_quota_reset.sh
• scripts/verification/verify_breaker.py
• scripts/watch_quota.sh
• start-stack.sh
• test_memory_mcp.py
• tests/test_a2_verify.py
• tests/test_agy_behavior.py
• tests/test_agy_tiers.py
• tests/test_antigravity.py
• tests/test_atomic_write.py
• tests/test_check_http_endpoint.py
• tests/test_circuit_breaker.py
• tests/test_classifier_accuracy.py
• tests/test_compute_free_model_score.py
• tests/test_host_agy_daemon.py
• tests/test_map_tool_to_category.py
• tests/test_models_proxy.py
• tests/test_pie_chart_gradient.py
• tests/test_record_tool_usage.py
• tests/test_src_badge.py
• tests/test_stream_latency.py
• tests/test_sync_gemini_token.py
• triage_upgrade_plan.md

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• Create PR with unit tests
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