[cucinellclark]

From cucinellclark/bvbrc_website:alpha-hardening into BV-BRC/BV-BRC-Web:alpha (up to date with
alpha, v3.60.7). 145 commits plus upstream merges; 58 files, +10.4k / −20.2k lines, nearly all under
public/js/p3/widget/copilot/ and resources/copilot.css.

This is the frontend for the multi-agent BV-BRC Copilot. It needs the matching Copilot API gateway
(BV-BRC-Copilot-API, branch alpha-hardening) and the Python orchestrator behind it. Older gateways
don't have the routes it calls (execution questions, session stop, workflow-watch status).

What users get

• Full-page chat at /view/Copilot, linked from the header (Tools & Services → AI → Chat). The
  floating window hides while the page is open.

• Plan / Execute mode. Nothing that writes (jobs, groups, group edits) runs without consent. In
  Plan mode the assistant prepares the job or group and asks one Yes / No / Other question
  (ExecutionBlockedCard):

  • Yes runs exactly what was shown.
  • No records the answer.
  • Other sends a change request.

  The answer survives reloads.

• Plans (PlanCard) with approve / skip / retry. A step that creates a group or submits a job
  pauses on its question, waits for submitted jobs, and continues when they finish.

• Clarifying questions as a card for every agent (ClarificationChips). The answers go back to
  the agent that asked.

• Live progress: a collapsed progress card while a turn runs, a "What I did" summary under each
  answer (ProgressView), and the view follows the card until the answer starts (TurnFollow).

• Job completion messages appear in the open chat without a reload.

• Workspace paths in answers become chips that open the workspace browser:

  • quoted or backticked paths keep their spaces;
  • links are URL-encoded per segment, so # and spaces work;
  • code blocks are left alone.

• Attachments: images (upload, paste, screenshot), text files and PDFs, plus a workspace file
  picker (CopilotWorkspacePathPicker).

• Large downloads from answers fetch every row with cursor paging (CursorDownload). In
  Chrome/Edge they stream to disk; the dialog explains the in-memory limit elsewhere.

• Smaller fixes:

  • jump-to-latest button, with "New response" when a reply finishes off-screen;
  • Stop works even before the first event arrives;
  • "Running" shown in the sidebar for background turns;
  • titles come from the first user message;
  • a new user's first chat is registered;
  • markdown images render as links (no automatic fetch);
  • the Copilot button shows when logged out, with a log-in prompt.

Removed

Code with no caller, or features the backend no longer supports:

• Legacy cards and their adapters: the data / workspace / jobs grid cards with their explorer
  adapters, CopilotToolHandler, the side-panel chat (ChatSessionContainerSidePanel,
  CopilotInputSidePanel), and the RAG dropdown.
• The old workflow form engine: WorkflowEngine.js (2,700 lines, imported but never
  constructed), its workflowForms/, and ServiceValidationRules.js.
• Hidden panels: the Files / Workflows / Images panels, which could no longer be opened but still
  fetched data on every chat switch. With them went their stores and the selection system.
  • The workflows "selection" was filled automatically from the session's job ids and sent with
    every message as items the user had selected. It no longer is.
  • Image chips in the input box are unchanged.
• Uncalled code: about 25 uncalled methods, and about 1,700 lines of CSS that only the removed
  code used.

Changes outside the Copilot folder (please review)

These are small and all Copilot-related; no other page's behaviour changes.

File	Change
widget/viewer/Copilot.js	The full-page chat viewer (was a stub)
app/p3app.js	Removed the old chat rectangle button; the floating button hides on /view/Copilot
views/bv-brc-header.ejs	"AI → Chat" menu entry
widget/GridContainer.js, widget/JobManager.js	Dropped imports of the removed side-panel chat
widget/WorkspaceObjectSelector.js	showHidden no longer throws when window.App is not set yet
store/ChatSessionsMemoryStore.js	Shared paging state for the session sidebar, and page merges deduplicated by session id

Testing

• Jest: 56 tests under public/js/p3/widget/copilot/tests/ pass.
• Release build (node dojo/dojo.js load=build --profile release.profile.js --release)
  completes. Its 28 errors are the pre-existing kinds: jest test files that aren't AMD modules, and
  libraries outside the build such as markdown-it, leaflet and molstar. None are in changed modules.
  The previous build of this branch reported 29; the difference is a deleted test file.
• Module loading: every p3/ module dependency resolves.
• ESLint: changed files have no new no-undef / no-unused-vars errors compared with alpha.
• Manual: run on our dev and public test sites (dev-8 / dev-6) with real users through
  October 2026.

🤖 Generated with Claude Code

[olsonanl]

#1475, #1474 and #1476 are now all on alpha (plus the v3.60.8 release), so this PR will
need a merge of alpha. I test-merged it to see what you're actually facing.

One conflict, one file, two hunks — both in the AMD block of GridContainer.js. No
function bodies conflict.

The resolution is not the usual "keep both sides", because this PR deletes
copilot/ChatSessionContainerSidePanel.js and alpha still imports it. Take alpha's list and
drop that one entry:

  './copilot/CopilotApi', './copilot/ChatSessionOptionsBarSidePanel',
  '../auth/authHeaders',
  '../util/QueryDescriptor',
  './download/UnifiedDownloadWizard',
  './download/SaveSearchDialog',
  '../util/joinTooBroad', './JoinTooBroadMessage',
  './ColumnsGenome', './AdvancedSearchFields', '../util/constructMetadataName', '../store/GenomeMetadataStore'
], function (
  …
  CopilotAPI, ChatSessionOptionsBar,
  authHeader,
  QueryDescriptor, UnifiedDownloadWizard, SaveSearchDialog,
  joinTooBroad, JoinTooBroadMessage,
  ColumnsGenome, AdvancedSearchFields, constructMetadataName, GenomeMetadataStore
) {

Everything else from alpha stays, including the searchColumnDefinitions block that follows
the factory opener — that's #1474's and unrelated to this PR.

I applied exactly that locally and verified: 43 deps / 43 params aligned, file parses,
and npm test passes 163/163 with all three feature sets present (your PlanCard,
#1475's joinTooBroad, #1474's searchColumnDefinitions).

One leftover worth knowing: line ~497 still has a commented-out
// this.chatPanel = new ChatSessionContainerSidePanel({. Harmless since it's a comment,
but you may want to clear it while you're in there given the module is gone.

After resolving, worth a quick arity check — a dep/param mismatch shifts every argument
after it and fails at runtime, not at merge:

node -e "const s=require('fs').readFileSync('public/js/p3/widget/GridContainer.js','utf8');
const m=s.match(/define\(\[([\s\S]*?)\]\s*,\s*function\s*\(([\s\S]*?)\)/);
const d=m[1].split(',').filter(x=>x.trim()).length, p=m[2].split(',').filter(x=>x.trim()).length;
console.log(d===p ? 'aligned ('+d+')' : 'MISALIGNED '+d+' deps vs '+p+' params')"