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added 2 commits
February 10, 2026 12:56
…owed for things like copy/pasting in the chatbot panel
…gs model while reindexing everything. Also added a keyword search fallback and made the documentation more relevant for users asking for help navigating the UI. Set a limit for number of search documentation calls
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I vote @samcraftt review cuz he has worked more recently with the agent implementation... |
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Pull request overview
This PR improves the in-app chatbot’s retrieval quality and grounding by reindexing documentation with a stronger embedding model + chunking, adding a keyword-search fallback, and tightening prompt/tooling rules to reduce hallucinations. It also expands file-management capabilities in the UI/backend (mount/unmount project directories, image previews, OS “reveal in folder”) and updates the chatbot’s documentation corpus to be end-user page guides rather than source-file summaries.
Changes:
- Rebuild RAG indexing (chunked documents, new embedding model), add keyword fallback, and cap documentation tool calls per user question.
- Replace code-oriented “file summaries” with end-user-focused page/workflow documentation used by the chatbot.
- Add File Manager mounting/unmounting + preview endpoints and corresponding UI/Electron integrations; adjust workflow selection modal behavior.
Reviewed changes
Copilot reviewed 53 out of 55 changed files in this pull request and generated 12 comments.
Show a summary per file
| File | Description |
|---|---|
| server_api/main.py | Uses a reset callback from build_chain() before chat queries/clears (replacing prior memory clearing behavior). |
| server_api/chatbot/update_faiss.py | Reindexes docs with chunking and a new embeddings model; saves updated FAISS index. |
| server_api/chatbot/chatbot.py | Updates prompts/routing rules, limits doc search calls, adds keyword fallback, changes embedding model default, and returns a reset function. |
| server_api/chatbot/faiss_index/index.pkl | Updated/added serialized FAISS docstore artifact committed to repo. |
| server_api/auth/router.py | Adds file preview endpoint, mount/unmount project directory endpoints, and safer recursive delete behavior. |
| server_api/auth/models.py | Adds MountDirectoryRequest schema for mount endpoint. |
| client/src/views/Views.js | Removes workflow preference persistence/polling and defaults workflow selector modal to open on startup. |
| client/src/views/FilesManager.js | Adds mounted project UX (mount/unmount, reveal-in-folder, mounted badges), image thumbnails via preview endpoint, and properties enhancements. |
| client/src/components/UnifiedFileInput.js | Simplifies browse flow to use mounted-storage picker (removes source selection modal). |
| client/src/components/FileTreeSidebar.js | Improves tree rendering/ellipsis styling for long names. |
| client/src/components/FilePickerModal.js | Adds upload-from-local, image-only filtering, and thumbnail previews in picker. |
| client/main.js | Adds standard Edit menu roles (cut/copy/paste/etc.) and IPC handler to reveal files in OS file explorer. |
| server_api/chatbot/file_summaries/views/ehtool/UnifiedImageEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ProofreadingEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ProgressTracker.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/LayerGrid.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/DetectionWorkflow.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/DatasetLoader.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ClassificationPanel.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/WormErrorHandling.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Visualization.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Views.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ProofReading.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Monitoring.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ModelTraining.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ModelInference.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/FilesManager.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/EHTool.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/main.md | Removed legacy server main summary from RAG corpus. |
| server_api/chatbot/file_summaries/contexts/YamlContext.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/contexts/GlobalContext.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/YamlFileUploader.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/YamlFileEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/WorkflowSelector.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/UnifiedFileInput.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/SynapseList.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/ProofreadingControls.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/NeuroglancerViewer.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/InputSelector.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/FileTreeSidebar.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/FilePickerModal.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/Configurator.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/Chatbot.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/api.md | Removed legacy API-client summary from RAG corpus. |
| server_api/chatbot/file_summaries/App.md | Removed legacy app root summary from RAG corpus. |
| server_api/chatbot/file_summaries/GettingStarted.md | Adds end-user “Getting Started” guide for overall app navigation. |
| server_api/chatbot/file_summaries/FileManager.md | Adds end-user File Manager workflow guide. |
| server_api/chatbot/file_summaries/Visualization.md | Adds end-user Visualization (Neuroglancer) workflow guide. |
| server_api/chatbot/file_summaries/ModelTraining.md | Adds end-user Model Training wizard/workflow guide. |
| server_api/chatbot/file_summaries/ModelInference.md | Adds end-user Model Inference wizard/workflow guide. |
| server_api/chatbot/file_summaries/Monitoring.md | Adds end-user TensorBoard Monitoring guide. |
| server_api/chatbot/file_summaries/Proofreading.md | Adds end-user SynAnno proofreading guide. |
| server_api/chatbot/file_summaries/ErrorHandlingTool.md | Adds end-user Error Handling Tool (EHT) workflow guide. |
| server_api/chatbot/file_summaries/WormErrorHandling.md | Adds end-user Worm Error Handling page guide. |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
8 tasks
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
6 tasks
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
[WIP] Update based on feedback for chatbot improvement PR
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
…nother-one [WIP] Update to improve chatbot functionality based on feedback
…gain Add input validation to /chat/query endpoint
samcraftt
reviewed
Feb 10, 2026
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| # Mount operation guardrails to prevent self-DoS |
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These changes seem unrelated to the chatbot and have to do with the file management functionality, right? If so, why are they necessary? @akgohain any thoughts on this since you were doing file management?
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I concur.....I'll pull in a bit and see if it's just an extra guardrail (then sure...fine) or if it's breaking
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It was something suggested by copilot during review, I think we could still move on without it but it's still good to have. Let me know what you think
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Also, you can follow the formatting steps in |
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Fixed the issue with crappy RAG retrievals by using a better embeddings model while reindexing everything. Also added a keyword search fallback and made the documentation more relevant for users asking for help navigating the UI. Set a limit for number of search documentation calls. Improved Chatbot prompts to reduce hallucination tendencies. Also allowed for things like copy/pasting in the chatbot panel