Fix backend-agent initialization for server-backed repositories

[madmansn0w]

Summary

This PR fixes the web app flow for server-backed repositories.

Previously, when connecting the web UI to a locally served GitNexus backend, the app still attempted to use the browser-local agent / embedding pipeline path. That caused failures such as:

• Database not ready. Please load a repository first.
• stalled Initializing Agent
• browser worker embedding startup running against a repo that was never loaded into the local WASM Kuzu instance

Root cause

The web app had two different repository modes, but the initialization path was still mixing them:

1. Browser-ingested repo mode

   • load repo into browser worker
   • initialize local agent
   • start browser embedding pipeline

2. Server-backed repo mode

   • fetch graph/file contents from backend
   • should initialize backend agent
   • should use backend-backed search/query capabilities

However, server-backed repositories were still calling the local initialization path in some cases, and the initial server connect flow also had a race where backend agent initialization could happen before serverBaseUrl state was available.

Changes

• added explicit isServerMode state to app state
• added initializeBackendAgent(...) to app state
• switched server connect flow to initialize the backend agent instead of the local browser agent
• passed the backend URL directly during initial server connection to avoid a React state timing race
• updated repo switching to use backend-agent initialization in server mode
• prevented browser-local embedding pipeline startup in server mode
• preserved browser embedding behavior for locally ingested repositories

Result

The web UI can now connect to a served backend repository without trying to run the browser-local embedding/database pipeline against a non-local repo.

This fixes the frontend/server-mode integration issue that produced:

• Database not ready. Please load a repository first.

Validation

Manually validated:

• connected web UI to local GitNexus server
• loaded a served repository successfully
• confirmed embeddings are available for the served repo
• confirmed AI chat path progresses past the previous DB-not-ready failure

Follow-ups / known issues

Not fixed in this PR:

• backend context-builder queries currently hit 404 for some /api/query-backed helper calls
• provider/auth configuration can still fail with 401 User not found depending on local LLM settings

[vercel]

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[reversTeam]

Thanks for the thorough PR, @madmansn0w! The problem statement and root-cause analysis are really clear. A few observations:

What looks good:

• The isServerMode flag is a clean way to bifurcate the two paths.
• Passing baseUrl directly into handleServerConnect to avoid the React state timing race is the right call.
• Guarding startEmbeddings with isServerMode early-return is simple and effective.
• The dependency arrays on useCallback are correctly updated throughout.

Issues / suggestions:

1. Inconsistent indentation in initializeBackendAgent — The function body (lines starting at const api = apiRef.current) is indented at 2 spaces instead of the 4 spaces used by the rest of useAppState.tsx. This looks like it was accidentally de-indented during editing.

2. Inconsistent indentation in switchRepo — Around the initializeBackendAgent call inside switchRepo, the indentation is mixed (some lines at 10 spaces, the closing brace at 8). Should be consistently 6 spaces to match the surrounding try block.

3. Duplicate setServerBaseUrl(baseUrl) call — In the auto-connect flow (useEffect), setServerBaseUrl(baseUrl) is called on line ~94 inside handleServerConnect, and then again on line ~94 of the .then() callback. The second call is redundant since handleServerConnect already sets it.

4. setEmbeddingStatus('ready') in switchRepo — When switching repos in server mode, you set embedding status to 'ready' directly. This is a reasonable shortcut since the backend handles search, but it could be confusing if other code checks embeddingStatus === 'ready' to mean "local embeddings are loaded." A comment explaining why this is safe would help future readers.

5. Lock file churn — The package-lock.json diff is large (~1000 lines) with esbuild version bumps. If these dependency updates aren't intentional, consider reverting the lock file to keep the diff focused.

6. No tests — Understandable for a React state hook, but the PR mentions known follow-up issues (404s on /api/query, 401 on auth). It would be good to track those as separate issues.

Overall this is a solid fix for a real pain point. The approach is sound — just needs the formatting cleanup and the duplicate setServerBaseUrl removed.

[madmansn0w]

Addressed in this update:

• Fixed indentation in initializeBackendAgent and switchRepo blocks in useAppState.tsx.
• Removed the redundant setServerBaseUrl(baseUrl) in auto-connect flow.
• Fixed onboarding server-connect call to pass both required args to handleServerConnect.
• Added a clarifying comment that embeddingStatus = 'ready' in server mode means backend search is ready (not local embeddings loaded).
• Reverted unintended dependency/lockfile churn to keep this PR focused.

Tracked follow-ups requested in review:

• 401 auth path: Server-mode backend agent returns 401 for authenticated backend calls #220
• 404 /api/query path: Server-mode backend flow returns 404 on /api/query #221

[magyargergo]

⚠️ Upcoming Prettier formatting — rebase instructions

PR #563 adds Prettier as the code formatter for the repo. When it merges, the bulk format commit will touch ~350 files (style-only: whitespace, quotes, trailing commas). Your branch will likely conflict.

After #563 merges, rebase your branch:

git fetch origin
git checkout <your-branch>
git rebase origin/main

# Conflicts will be formatting-only — accept your version:
git checkout --theirs .
git add .
git rebase --continue

# Then re-format your branch to match the new style:
npx prettier --write .
git add -A
git commit -m "style: apply prettier formatting"
git push --force-with-lease

New setup step: Run npm install at the repo root (not just in gitnexus/) to get prettier + activate the pre-commit hook. The hook auto-formats staged files on every commit going forward.

[magyargergo]

Please submit a new PR if this is still relevant