chore: reorganize repo code to make into domain specific directories and improve test coverage to prevent regressions

[Colin Francis (colifran)]

Summary

Refactor phase 1: this reorganizes the code base into more logical domain specific directories with increased code coverage. This structure will allow humans and agents to contribute more meaningfully, allow for faster reviews, and will help prevent against regressions due to higher test coverage.

Next phases will focus on splitting cli.tsx and credentials.tsx.

Repo structure

Before: 18 loose files at src/ root, flat test/ (63 of 64 files at top level), no coverage config.

Before (main):

src/
  agent/
  auth/
  connectors/
  mermaid/
  okf/
  telemetry/
  visualize/
  cli.tsx
  code-mode.ts
  commands.ts
  constants.ts
  credentials.tsx
  diagnostics.ts
  env.ts
  external-cli-auth.ts
  fs-errors.ts
  ingestion.ts
  language.ts
  onboarding.ts
  openwiki-home.ts
  schedules.ts
  startup.ts
  utils.ts
  version.ts
  windows-acl.ts
test/
  (flat: 63 of 64 files at top level)

After (this branch):

src/
  agent/
  auth/          (+ external-cli-auth)
  cli/           (cli, commands, startup)
  config/        (constants, env, openwiki-home)
  connectors/
  ingestion/     (ingestion, code-mode)
  mermaid/
  okf/
  platform/      (diagnostics, fs-errors, language, utils, windows-acl)
  scheduling/    (schedules)
  setup/         (credentials, onboarding)
  telemetry/
  visualize/
  version.ts
test/            (mirrors src/ one-to-one)
vitest.config.ts (all:true honest coverage)

Coverage

Both columns measured under this PR's all:true vitest config so they compare directly.

Metric	Before	After
Statements	40.09%	57.83%
Branches	34.78%	51.91%
Functions	45.88%	63.47%
Test files / tests	64 / 768	93 / 1290

Tooling

pnpm check removed and folded into pnpm test and CONTRIBUTING.md has been updated.

Testing

New unit tests to increase coverage. All existing tests pass.

[changeset-bot]

🦋 Changeset detected

Latest commit: 4be0fc1

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
openwiki	Patch

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