Sync and harden the TOCHI agentic prototype

[akgohain]

What changed

• harden frontend API URL construction for reverse-proxy and legacy /api prefixes
• add backend compatibility routing for deployed API paths
• improve Neuroglancer image-layer construction and demo rendering defaults
• protect project context from accidental mutation when users reference volume IDs
• improve Yixiao project defaults, progress explanations, smoke reporting, and health checks
• add focused frontend/backend tests and case-study/deployment documentation

Why

The deployed TOCHI prototype accumulated operational fixes after the June 3 checkpoint. Those fixes existed only in the demo2 working tree, leaving GitHub unable to reproduce the most deployment-correct prototype state.

User and developer impact

The checkpoint branch now reflects the curated demo source, tests, runbooks, and authored case-study documentation from the deployed prototype. Generated smoke reports and screenshots remain local because they contain transient viewer URLs and machine-specific evidence.

Root causes addressed

• public reverse-proxy paths could duplicate API prefixes
• compatibility paths were not normalized consistently across frontend and backend
• workflow questions containing identifiers such as 5_1 could be misread as project-context values
• Neuroglancer image and segmentation layers needed explicit construction behavior
• post-deploy verification was not captured as a reusable health-check contract

Validation

• 9 passed: focused Neuroglancer and workflow-agent backend tests
• 5 passed: Yixiao pre-demo smoke tests
• 6 passed: frontend API/log canonicalization tests
• Python compilation passed for all changed Python modules and tests
• git diff --check passed

Known limitation: the broader API compatibility integration test currently hangs on the /files request in this environment and needs follow-up before this draft is considered merge-ready.

Review note

This is a draft integration anchor. The checkpoint branch has substantial historical divergence from main, including overlapping project-management directions, so it should not be merged wholesale without a separate reconciliation pass.