chore: remove unused files, dependencies, and exports flagged by knip (#1982)

## Summary

Cleans up dead code and unused dependencies identified by [knip](https://knip.dev/). All removals were individually verified to have zero imports or references across the codebase. No functional changes.

**Deleted 9 unused files:**
- `packages/api/src/clickhouse/__tests__/clickhouse.V1_DEPRECATED_test.ts` — skipped deprecated test
- `packages/api/src/utils/email.ts` — empty stub functions, never imported
- `packages/api/src/utils/queue.ts` — unused utility class
- `packages/app/src/Checkbox.tsx` — replaced by Mantine Checkbox, never imported
- `packages/app/src/components/DBSearchPageFilters/index.ts` — dead barrel file (shadowed by sibling `.tsx`)
- `packages/app/src/components/Sources/index.ts` — dead barrel file (all consumers import submodules directly)
- `packages/app/src/components/WhereLanguageControlled.tsx` — unused component
- `packages/app/src/TabBarWithContent.tsx` — unused component
- `packages/app/src/vsc-dark-plus.ts` — unused Prism theme

**Removed 14 unused dependencies** from `packages/api`, `packages/app`, and `packages/common-utils` (e.g. `semver`, `react-query`, `react-sortable-hoc`, `@microsoft/fetch-event-source`, `store2`, `uuid`, etc.)

**Removed 17 unused devDependencies** across root, api, app, and common-utils (e.g. `@nx/workspace`, `@typescript-eslint/eslint-plugin`, `@typescript-eslint/parser`, `@types/semver`, `@types/react-table`, `rimraf`, `supertest`, `ts-node`, `tsc-alias`, `tsconfig-paths`, etc.)

**Replaced `react-papaparse` with `papaparse`** — code imports `papaparse` directly, not the React wrapper. Added `@types/papaparse` since the package doesn't bundle its own types.

**Cleaned up unused exports:**
- Trimmed barrel files (`AppNav/index.ts`, `SearchInput/index.ts`) to only re-export what's actually consumed
- Removed duplicate named exports where only the default export is used (`DBRowTableFieldWithPopover`, `DBRowTableRowButtons`)
- Un-exported interfaces and constants that are only used locally (`DBRowTableFieldWithPopoverProps`, `DBRowTableIconButtonProps`, `DBRowTableRowButtonsProps`, `BASE_URL`, `makeHandler`)
- Removed stale `supertest` from `allowModules` in `common-utils/eslint.config.mjs`

### How to test locally or on Vercel

1. `yarn install` — lockfile should resolve cleanly
2. `yarn workspace @hyperdx/common-utils ci:lint` — should pass (the only package where lint+tsc fully passes on this branch)
3. `npx knip` — should show reduced issue counts vs. main

### References

- Related PRs: #1973 (knip CI workflow)

Author: brandon-pereira

package.json

@@ -9,10 +9,7 @@
   "devDependencies": {
     "@changesets/cli": "^2.26.2",
     "@dotenvx/dotenvx": "^1.51.1",
-    "@nx/workspace": "21.3.11",
     "@types/ungap__structured-clone": "^1.2.0",
-    "@typescript-eslint/eslint-plugin": "^8.48.1",
-    "@typescript-eslint/parser": "^8.48.1",
     "@ungap/structured-clone": "^1.3.0",
     "babel-plugin-react-compiler": "^1.0.0",
     "concurrently": "^9.1.2",

packages/api/package.json

@@ -46,15 +46,13 @@
     "pino-http": "^11.0.0",
     "promised-handlebars": "^2.0.1",
     "protobufjs": "^7.5.2",
-    "semver": "^7.5.3",
     "serialize-error": "^8.1.0",
     "uuid": "^8.3.2",
     "zod": "3.25",
     "zod-express-middleware": "^1.4.0"
   },
   "devDependencies": {
     "@stoplight/spectral-cli": "^6.15.0",
-    "@types/aws4": "^1",
     "@types/compression": "^1.7.3",
     "@types/cors": "^2.8.14",
     "@types/express": "^4.17.13",
@@ -64,7 +62,6 @@
     "@types/minimist": "^1.2.2",
     "@types/ms": "^0.7.31",
     "@types/passport-local": "^1.0.34",
-    "@types/semver": "^7.3.12",
     "@types/supertest": "^2.0.12",
     "@types/swagger-jsdoc": "^6",
     "@types/uuid": "^8.3.4",