Update pyinstaller requirement from >=6.16.0 to >=6.21.0 in /notebooks - #30

These files came from a generic polyglot project template
(Tauri-App-Template) and assumed a multi-language monorepo with
Python/Kotlin/Java/Rust/Go/C++ modules, cloud infra, and multi-host
CI. This repo is a single-language Next.js/React/TypeScript static
site deployed to GitHub Pages, plus a small Python/uv notebooks
workspace for report research — so the irrelevant pieces are removed:

- .forgejo/, .gitea/, .gitlab/: not hosted on those platforms
- cloud/, infra/: no cloud/container infra for a static export site
- git/: GitHub Project board automation and generic template CONTRIBUTING
- docs/{ARCHITECTURE,BENCHMARKS,DEPENDENCIES,DEPENDENCY_POLICY,
  DEVELOPMENT,DOCUMENTATION_STANDARDS,GLOSSARY,TESTING,TROUBLESHOOTING}.md,
  docs/adr/, docs/moon/{ROADMAP,CHANGELOG}.md, docs/moon/roadmaps/:
  described modules/roadmaps that don't exist here
- .agent/rules/{go,kotlin,java,cpp,rust,ai_ml}.md,
  .agent/workflows/{rust,data_eng,ai_ml,deployment_ops}.md,
  .agent/skills/add-language-module.md,
  .agent/prompts/cli_generation.md: languages/workflows unused here

The two genuine research write-ups under docs/moon/research and
docs/moon/reports move to docs/research/ since they're real content
about this project, not template placeholders.

- ci.yml: replace the polyglot lint/test/build matrix with lint + tsc
  + jest + cypress + a next build check, plus a light ruff pass over
  notebooks/.
- security.yml: npm audit + pip-audit (uv) for notebooks/, drop
  cargo-audit.
- Remove agent_sync.yml (GitHub Project board automation tied to the
  deleted git/ scripts) and docs.yml (no MkDocs site here).
- Issue/PR templates: swap the language-module dropdown for the
  site's actual content areas (posts/reports/projects/tools/etc).
- dependabot.yml: add npm and uv (notebooks/) ecosystems alongside
  the existing github-actions one; bump cadence to weekly.
- .pre-commit-config.yaml: eslint/tsc for the site, ruff/mypy for
  notebooks/, drop the other five language toolchains.
- .devcontainer: Node + Python(uv) only, drop Rust/Go/JVM toolchains.
- pyproject.toml: fix license file reference (LICENSE, not LICENSE.md).

AGENTS.md, the TS/React and Python rule files, the build-and-test and
debug-crash skills, and the master_context/architecture_analysis/
documentation_update/feature_implementation prompts all described a
generic polyglot template (multi-language modules, Vitest, Tauri,
MkDocs, just recipes). Rewritten to reflect what's actually here: a
static-export Next.js/React/TypeScript site with Jest+Cypress tests,
and a small notebooks/ Python-uv workspace for report research.

Also swapped the domain-specific examples in the six subagent
delegation protocol files (Rust/C++ refactors, PySide6 GUIs, RL reward
functions, OpenCV bindings) for ones grounded in this repo — drafting
report prose, reviewing notebook analysis code, refactoring React
components — while keeping the PCVRP example where it already matched
an existing report.

Not part of the intended cleanup; unrelated content that ended up
staged alongside the .agent/ changes.

Replace the plain tech list and course-template boilerplate with a
badge-based header (stack + CI/deploy status + license), a project
structure overview, and concrete getting-started/testing/deployment
instructions, following the style of Image-Toolkit/nglab/WSmart-Route.

Restored copies of .forgejo/, .gitea/, .github/, .gitlab/, and git/
still described a polyglot python/typescript/kotlin/java/rust/go/cpp
project and referenced the source template by name. Rewritten so every
file reflects only this repository:

- ci.yml (all three CI hosts) and .gitlab-ci.yml: lint/typecheck/jest/
  cypress/build for the Next.js site, ruff for notebooks/ — no
  cargo/gradle/mvn/cmake/go steps.
- security.yml: npm audit + pip-audit only.
- benchmark.yml: Lighthouse against the static export, no explanatory
  commentary about what it replaces.
- docs.yml / docs-link-check: a real lychee link-check job over docs/,
  not a manual no-op with a "restore this later" comment.
- agent_sync.yml / agent-sync.yml / the sync stage in .gitlab-ci.yml:
  same real job on every host — it only ever talks to GitHub's
  Projects (V2) API regardless of which CI runs it, so the
  "not portable to Forgejo/Gitea/GitLab" guard was wrong and is gone.
- Issue/PR/MR templates: content-area dropdown instead of a
  language-module dropdown, on every host.
- git/CONTRIBUTING.md, git/README.md, git/config/*, git/hooks/*,
  git/scripts/*: rewritten/restored with no template name, no
  "ported from <other repo>" attribution, and a component label set
  (site/content/notebooks/ci-automation/docs) that matches this repo
  instead of one label per unused language.

None of this repo's directories were removed. A handful of files with
zero applicability to this project (per-language rule/roadmap files,
the template's own dev-tool roadmap) were deleted outright rather than
kept with a "not applicable" banner, per explicit instruction.

- git/pyproject.toml: declare the git scripts' actual runtime deps
  (pyyaml, requests, google-genai) and a setuptools build so `scripts`
  is installable as a package, matching sync_backlog.py/
  check_commit_ref.py now importing agent_tools via a relative import
  (`from .agent_tools import ...`), which requires running as
  git.scripts.<module> rather than as a bare script.
- Register "git" as a uv workspace member alongside "notebooks" in the
  root pyproject.toml.
- Update every agent_sync/agent-backlog-sync CI job (GitHub, Gitea,
  Forgejo, GitLab) to `uv sync --project git` and invoke
  `python -m git.scripts.sync_backlog` instead of a direct file path.
- Update git/hooks/post-commit and post-commit.bat the same way for
  check_commit_ref.py, using `uv run --project git` from the repo root.

docs/*.md, docs/adr/0001, docs/moon/ROADMAP.md, docs/moon/CHANGELOG.md,
and three of the docs/moon/roadmaps/ files had been emptied out to
clear any remaining template content. Written fresh, describing only
this repository:

- docs/*.md: architecture, dependencies, dev setup, testing,
  troubleshooting, docs standards, glossary, benchmarks — all for the
  actual Next.js + notebooks/ + git/ stack, no leftover framing about
  what any of this used to describe.
- docs/adr/0001: restored (generic ADR practice, no template content).
- docs/moon/ROADMAP.md: now points at per-theme roadmaps instead of
  a scaffolding-adoption tracker.
- docs/moon/roadmaps/{user_interface,interactive_features,
  mathematical_optimization,machine_learning,documentation}.md:
  rewritten as a forward-looking, feature-themed roadmap for the site
  (3D/motion UI, interactive graphics, an in-browser PCVRP demo,
  client-side ML, docs upkeep), drawing on docs/moon/research/.
- cloud/aws/cfn-template.yaml, cloud/azure-pipelines/azure-pipelines.yml,
  cloud/serverless/serverless.yml: real, working configs to deploy the
  static export to AWS (S3 + CloudFront, via CloudFormation or the
  Serverless Framework) and Azure Static Web Apps, as alternatives to
  the GitHub Pages deploy this repo actually uses.

Replaced the inherited Python+Postgres+Redis backend stack with
infra that actually deploys this repo: build the Next.js static
export and serve it via nginx.

- infra/docker/: Dockerfile now does npm run build then serves out/
  via nginx (new nginx.conf); docker-compose.yml/prod.yml drop the
  db/redis services down to a single `site` service; removed
  entrypoint.sh (no database to wait for).
- infra/k8s/: Deployment/Service/Ingress renamed from
  tauri-app-template to github-pages, port 8000 -> 80, readiness
  probe points at `/`; removed the ConfigMap (nothing left to
  configure via env vars).
- infra/helm/: renamed the tauri-app-template/ chart directory to
  github-pages/ and updated Chart.yaml/values.yaml/templates to
  match; removed its ConfigMap template too.
- infra/terraform/: provisions a real aws_ecr_repository for the
  built image instead of an empty placeholder; project_name/bucket
  names updated from tauri-app-template to github-pages.
- infra/ansible/: role now installs Docker and runs the built image
  directly instead of templating a .env file for a Python app.
- Every README rewritten to describe what's actually here, with no
  "not currently used"/"dormant"/"inherited from the template"
  framing.

- Add vitest, @vitejs/plugin-react, jsdom, msw, @testing-library/user-event;
  remove jest, jest-environment-jsdom, ts-jest, @types/jest.
- vitest.config.ts: jsdom environment, @/* alias matching tsconfig,
  globals enabled, CSS processing disabled (the repo's postcss.config.js
  uses Next.js-style string plugin names Vite's loader can't resolve).
- test/vitest.setup.ts: jest-dom matchers plus MSW server lifecycle
  (see the next commit for the integration tests that use it).
- Move src/components/__tests__/*.test.tsx to test/unit/components/,
  mirroring the src/components/{layout,ui}/ layout, converting
  jest.fn()/jest.mock() to vi.fn()/vi.mock().
- package.json: test -> vitest run, test:watch -> vitest, plus new
  test:unit/test:integration scripts.

All 9 suites (25 tests) pass under `npm run test:unit`.

- layout.integration.test.tsx: mounts ClientLayoutWrapper (Header +
  Sidebar + Footer together) and verifies the theme toggle and
  localStorage persistence flow across all three.
- navigation-active-state.integration.test.tsx: verifies a pathname
  change flows through ClientLayoutWrapper's getActiveSection into the
  correct Sidebar item being marked active.
- github-profile.integration.test.ts: exercises the MSW-backed network
  layer itself (default handler, per-test override, and that a truly
  unhandled request is rejected instead of hitting the real network).

Also fixes two environment issues surfaced by these tests:
- vitest.config.ts: set environmentOptions.jsdom.url so jsdom's APIs
  that require an origin work correctly.
- test/vitest.setup.ts: Node's own built-in `localStorage` global
  (stable since Node 22) shadows jsdom's window.localStorage with a
  non-functional stub when no --localstorage-file is configured;
  replaced with a small in-memory Storage polyfill, reset between
  tests.

12 test files, 33 tests, all passing under `npm test`.

- test/cypress/e2e/*.cy.js: moved as-is (2 pre-existing failures in
  navigation.cy.js/other.cy.js predate this move, matching the stale
  failure screenshots that were committed alongside them).
- test/cypress/cypress.config.js: moved from repo root; specPattern
  now covers both e2e/ and smoke/, explicit screenshots/videos folders.
- test/cypress/smoke/: new — smoke.cy.js checks every top-level route
  renders the header/main/footer shell and the homepage logs no
  console errors; theme-toggle.cy.js checks the dark/light toggle.
- Dropped the committed cypress/screenshots/ failure artifacts and
  gitignored test/cypress/{screenshots,videos}.
- package.json: cypress:open/run/e2e/smoke scripts now `cd
  test/cypress` first — Cypress resolves --spec relative to cwd
  regardless of --config-file/--project, so that's the only way to
  point it at the moved specs.

Verified against a running `npm run dev`: 10/10 smoke tests pass,
8/10 e2e tests pass (the 2 pre-existing failures unchanged).

- CI (GitHub, Gitea, Forgejo, GitLab): run test:unit + test:integration
  instead of the old jest --ci --coverage invocation; Cypress steps use
  working-directory: test/cypress (GitHub-style action) or `cd
  test/cypress` (GitLab), since Cypress resolves spec globs relative to
  the current working directory regardless of --config-file/--project.
- tsconfig.json: add "types": ["vitest/globals"] so `tsc --noEmit`
  (used by CI and the pre-commit hook) recognizes describe/it/expect/vi
  in test files instead of erroring on every one of them.
- package.json: postbuild script symlinks out/github-pages -> . so a
  plain `serve` of the static export answers under the /github-pages
  basePath locally, the same way GitHub Pages does — needed for the
  Cypress and Lighthouse CI jobs that serve the production build.
- docs/TESTING.md, docs/DEVELOPMENT.md, docs/TROUBLESHOOTING.md,
  README.md, git/CONTRIBUTING.md, .agent/{AGENTS.md,rules/
  typescript_react.md,skills/{build-and-test,debug-crash}.md,prompts/
  feature_implementation.md}: replaced every Jest/root-cypress
  reference with the Vitest/RTL/MSW/test-cypress equivalents.
- docs/moon/CHANGELOG.md: logged the migration; docs/moon/ROADMAP.md:
  updated the S3 item; docs/moon/roadmaps/infrastructure_and_testing.md:
  filled in with what's done (Vitest migration, MSW integration tests,
  Cypress move + smoke tests, the postbuild basePath fix, CI wiring)
  and what's left (coverage reporting, two pre-existing e2e failures).
- .gitignore: test/cypress/{screenshots,videos}, *.tsbuildinfo.

Full `npm run lint && npx tsc --noEmit && npm test && npm run build`
passes.

docs/website/react/, following the pattern of the docs/website/vue
site in Project-Mobile-Fortress (a documentation portal + component
catalogue for the repo), but built from a different stack per this
project's actual needs:

- Docusaurus (classic preset) serves this repo's docs/ directly (no
  copy step — the docs-plugin's `path` points straight at ../../) plus
  a curated set of outside-docs guides (README.md, git/CONTRIBUTING.md,
  .agent/AGENTS.md) on a second plugin instance.
- TypeDoc + typedoc-plugin-markdown generates API reference for lib/'s
  exported functions/types (`npm run gen:api`), registered on the same
  docs-plugin instance as the rest of docs/ since it's physically
  nested there.
- Storybook (@storybook/react-vite) renders the real src/components/
  sources (via a site-src/ symlink, not a copy) with a dark/light
  theme toggle and Tailwind wired in for accurate styling; Next.js-only
  imports (next/image, next/link, next/navigation) get small shims
  since this runs on plain Vite.
- `npm run build` chains gen:api -> build-storybook -> docusaurus
  build -> copies the Storybook output into build/storybook/, so the
  whole dashboard ships as one static site.

Two real upstream issues surfaced and worked around, documented inline
where they're worked around and in react/README.md's "Notable
implementation gotchas":
- A Docusaurus 3.10 bug mis-resolves the webpack import for a doc
  whose docs-plugin `include` lists it under a *different* plugin
  instance's `path` than where it's physically nested — fixed by
  registering the generated API docs on the plugin instance that
  actually owns docs/ on disk.
- vite-plugin-react-docgen-typescript (Storybook's prop-table
  generator) never attaches docgen info to files outside its own
  project directory, symlink or no — every story ships hand-written
  argTypes (control + description per prop) as a working substitute,
  documented as a known limitation rather than papered over.

Also pinned lucide-react to 0.469.0 (React 19 support with the same
icon names as the main site's 0.383.0) and Vite to ^5 (the default
Vite 8 that @storybook/react-vite pulls in fails to parse JSX in a few
story files).

You were right to question it: the symlink (ln -s ../../../src
site-src) existed solely to try to get vite-plugin-react-docgen-typescript
to treat the real src/components/ files as inside this project, but it
never actually worked — docgen still skipped every component with the
symlink in place (verified before this change: 8 "not included in the
active TypeScript project" warnings either way). So it bought nothing
and just added a layer of indirection to explain.

Stories now import straight from ../../../../src/components/... with
no symlink involved. Simplified .storybook/main.ts back to a plain
alias map (no preserveSymlinks, no alias-ordering workaround needed
now that there's no @/site-src vs @ collision to avoid). Updated both
READMEs' "how it works" sections and global.d.ts's comment to match.

Verified: npm run typecheck and the full npm run build (TypeDoc ->
Storybook -> Docusaurus -> merge) both still pass.

Updates the requirements on [pyinstaller](https://github.com/pyinstaller/pyinstaller) to permit the latest version.
- [Release notes](https://github.com/pyinstaller/pyinstaller/releases)
- [Changelog](https://github.com/pyinstaller/pyinstaller/blob/develop/doc/CHANGES.rst)
- [Commits](pyinstaller/pyinstaller@v6.16.0...v6.21.0)

---
updated-dependencies:
- dependency-name: pyinstaller
  dependency-version: 6.21.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>