feat: robust GitHub issue tracking + user feedback UI

.github/CODEOWNERS

@@ -0,0 +1,10 @@
+# Default owner for everything in this repo.
+* @VibhavSetlur
+
+# Infrastructure / release surface — keep an explicit owner.
+/.github/ @VibhavSetlur
+/.github/workflows/ @VibhavSetlur
+
+# Feedback / issue-tracking UI added in this change.
+/components/feedback/ @VibhavSetlur
+/app/api/feedback/ @VibhavSetlur

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,116 @@
+name: Bug report
+description: Something is broken or behaving unexpectedly in the ModelSEED web app.
+title: "[Bug]: "
+labels: ["bug", "triage"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting a bug! Please describe what went wrong in your own words —
+        no technical knowledge required. Fields marked with an asterisk are required.
+
+  - type: dropdown
+    id: environment
+    attributes:
+      label: Which site were you using?
+      options:
+        - "staging.modelseed.org (staging)"
+        - "modelseed.org (production)"
+        - "localhost / dev"
+        - "Not sure"
+    validations:
+      required: true
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Which part of the app?
+      options:
+        - FBA
+        - Gapfill
+        - Model viewer
+        - Biochem browser
+        - Media
+        - Genomes
+        - My Jobs / My Models
+        - Auth / Sign-in
+        - Other
+    validations:
+      required: true
+
+  - type: dropdown
+    id: auth_status
+    attributes:
+      label: Were you signed in?
+      options:
+        - "Signed in (PATRIC / BV-BRC)"
+        - "Signed in (RAST)"
+        - "Not signed in"
+        - "Not sure"
+    validations:
+      required: true
+
+  - type: textarea
+    id: what_happened
+    attributes:
+      label: What happened?
+      description: Describe the problem you saw, in your own words.
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: What did you expect to happen instead?
+    validations:
+      required: false
+
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to reproduce
+      description: "List what you did, e.g. 1) opened FBA, 2) selected model X, 3) clicked Run."
+    validations:
+      required: false
+
+  - type: input
+    id: model_ref
+    attributes:
+      label: Model / object reference (if relevant)
+      description: "e.g. a model id, workspace path, or reaction/compound id."
+    validations:
+      required: false
+
+  - type: textarea
+    id: screenshots
+    attributes:
+      label: Screenshots
+      description: Drag and drop or paste any screenshots here.
+    validations:
+      required: false
+
+  - type: input
+    id: browser
+    attributes:
+      label: Browser & OS
+      description: "e.g. Chrome 130 on macOS, Firefox on Windows."
+    validations:
+      required: false
+
+  - type: textarea
+    id: console
+    attributes:
+      label: Console errors (optional)
+      description: "If comfortable, paste any red errors from the browser dev-tools console."
+      render: shell
+    validations:
+      required: false
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Before you submit
+      options:
+        - label: I searched existing issues and did not find a duplicate.
+          required: false

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,11 @@
+blank_issues_enabled: false
+contact_links:
+  - name: ModelSEED documentation & help
+    url: https://modelseed.org/
+    about: Browse ModelSEED docs and the app's built-in help before filing an issue.
+  - name: Ask on the ModelSEED mailing list
+    url: https://modelseed.org/
+    about: For broad usage or research questions, the mailing list may be a better fit.
+  - name: Security disclosure (do not open a public issue)
+    url: https://github.com/ModelSEED/ModelSEED-UI/security/advisories/new
+    about: Report a security vulnerability privately via GitHub Security Advisories.

.github/ISSUE_TEMPLATE/documentation.yml

@@ -0,0 +1,55 @@
+name: Documentation improvement
+description: Report missing, unclear, or incorrect documentation or in-app help text.
+title: "[Docs]: "
+labels: ["documentation", "triage"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Help us improve the docs and in-app guidance. Point us at what was confusing.
+
+  - type: dropdown
+    id: doc_location
+    attributes:
+      label: Where is the documentation problem?
+      options:
+        - In-app help / tooltip text
+        - About / version pages
+        - README or repository docs
+        - API documentation
+        - Team / contact info
+        - Other
+    validations:
+      required: true
+
+  - type: input
+    id: page_url
+    attributes:
+      label: Page or URL (if applicable)
+      description: "e.g. https://modelseed.org/about or a repo file path."
+    validations:
+      required: false
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: What is missing, unclear, or wrong?
+    validations:
+      required: true
+
+  - type: textarea
+    id: suggestion
+    attributes:
+      label: Suggested improvement
+      description: How would you word or structure it instead?
+    validations:
+      required: false
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Before you submit
+      options:
+        - label: I searched existing issues and did not find a duplicate.
+          required: false

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,77 @@
+name: Feature request
+description: Suggest a new capability or an improvement to the ModelSEED web app.
+title: "[Feature]: "
+labels: ["enhancement", "triage"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for the idea! Tell us what you'd like to be able to do and why it would help.
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Which part of the app is this about?
+      options:
+        - FBA
+        - Gapfill
+        - Model viewer
+        - Biochem browser
+        - Media
+        - Genomes
+        - My Jobs / My Models
+        - Auth / Sign-in
+        - New / general idea
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: request
+    attributes:
+      label: What would you like to be able to do?
+    validations:
+      required: true
+
+  - type: textarea
+    id: use_case
+    attributes:
+      label: What's your use case?
+      description: Describe the workflow or research task this would support.
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives or workarounds you've tried
+    validations:
+      required: false
+
+  - type: dropdown
+    id: priority
+    attributes:
+      label: How important is this to you?
+      options:
+        - Nice to have
+        - Would help a lot
+        - Blocking my work
+    validations:
+      required: true
+
+  - type: textarea
+    id: examples
+    attributes:
+      label: Examples, sketches, or screenshots
+      description: Anything that shows what you have in mind. You can drag images in here.
+    validations:
+      required: false
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Before you submit
+      options:
+        - label: I searched existing issues and did not find a duplicate request.
+          required: false

.github/ISSUE_TEMPLATE/question.yml

@@ -0,0 +1,56 @@
+name: Question
+description: Ask a question about using the ModelSEED web app or interpreting results.
+title: "[Question]: "
+labels: ["question", "triage"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Ask anything about the app, the data, or how something works. If it turns out to be
+        a bug or feature idea, we'll route it from here. No technical knowledge needed.
+
+  - type: dropdown
+    id: environment
+    attributes:
+      label: Which site are you using?
+      options:
+        - "staging.modelseed.org (staging)"
+        - "modelseed.org (production)"
+        - "localhost / dev"
+        - "Not sure"
+    validations:
+      required: false
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Which part of the app is your question about?
+      options:
+        - FBA
+        - Gapfill
+        - Model viewer
+        - Biochem browser
+        - Media
+        - Genomes
+        - My Jobs / My Models
+        - Auth / Sign-in
+        - Not sure / general
+    validations:
+      required: false
+
+  - type: textarea
+    id: question
+    attributes:
+      label: What would you like to know?
+      description: "Ask in your own words."
+    validations:
+      required: true
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Anything else that would help us answer?
+      description: "You can drag in a screenshot of what you're looking at."
+    validations:
+      required: false

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,41 @@
+## Summary
+
+<!-- What does this PR change and why? Link any related issue: Closes #123 -->
+
+## Type of change
+
+- [ ] Bug fix (non-breaking change that fixes an issue)
+- [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that changes existing behavior)
+- [ ] Documentation / chore / CI
+
+## Affected area(s)
+
+<!-- e.g. FBA, Gapfill, Model viewer, Biochem browser, Media, Genomes, Auth, .github -->
+
+## Release flow awareness
+
+This repository ships **staging → production**:
+
+- [ ] This PR targets `ModelSEED/ModelSEED-UI:staging` (not `master`).
+- [ ] I understand staging is validated on **staging.modelseed.org** before it is merged
+      to `master` and deployed to **modelseed.org** by a maintainer.
+- [ ] This PR does **not** push directly to `upstream` `master`.
+
+## Verification (must mirror CI — `.github/workflows/ci.yml`)
+
+Run in the project conda env and check each:
+
+- [ ] `npm run lint`
+- [ ] `npx tsc --noEmit`
+- [ ] `npm run test:run`
+- [ ] `npm run build`
+- [ ] `npm audit --omit=dev --audit-level=high`
+
+## Screenshots / recordings (UI changes)
+
+<!-- Before / after for any user-facing change. -->
+
+## Notes for reviewer
+
+<!-- Anything the reviewer should focus on, deploy caveats, follow-ups. -->

.gitignore

@@ -1,4 +1,5 @@
 # Local
+,claude/
 /legacy/
 PRODUCTION_POLISH_PLAN.md
 scripts/local
@@ -72,3 +73,6 @@ CLAUDE.local.md
 .opencode/
 .gsd/.opencode/
 .build-date
+.claude/
+.omo/
+GEMINI.md