docs: fill Harper-specific gaps surfaced by skills reverse-scan

[kriszyp]

Summary

A reverse gap-scan of the harper-best-practices skill rules against the docs surfaced Harper-specific patterns the rules teach but the docs don't. The first migrated rule (vector-indexing) lost two such patterns when it was regenerated from reference/database/schema.md#vector-indexing — this PR closes those gaps and several more so the docs-driven pipeline can take other rules without quality regressions.

Each addition was verified against Harper core source before documenting; nothing here is invented.

Changes

• Vector indexing (reference/database/schema.md): distance-threshold filter (conditions[].target + comparator: 'lt') and the $distance special select field. Closes the regression introduced by feat: Phase 2 — docs-driven rule generator (generate + direct modes) skills#38.
• Blob handling (reference/database/api.md): full BlobCreationOptions table (type, size, compress, flush, saveBeforeCommit), base64-from-JSON intake pattern, and the standard Content-Type + body: blob response shape for serving binary.
• getCurrentUser() + Session/Login from a Resource (reference/resources/resource-api.md): documents getCurrentUser(), Context.login, and Context.session.delete so custom Resources can implement sign-in flows.
• JWT issuance from a custom Resource (reference/security/jwt-authentication.md): adds an IssueTokens / RefreshJWT recipe using server.operation() (rather than reaching into system tables). Closes Document JWT issuance via databases.system.hdb_user.operation #501.
• $distance in Query Object (reference/resources/resource-api.md): added alongside $id and $updatedtime in the select reference.
• Resource routing via export shape (reference/resources/overview.md): a table mapping export class Foo, export const Bar = { Foo }, and export const bar = { 'foo-baz': Foo } to the resulting URLs, plus a note that path matching is case-sensitive.
• Extending tables (reference/resources/overview.md): explicit "omit @export" guidance and the super.* call convention.
• TypeScript support (reference/components/javascript-environment.md): Harper's Node-native type stripping — Node ≥ 22.6, .ts source files, explicit .ts in local imports, jsResource glob.
• Logging (reference/logging/api.md): describe console capture semantics accurately (stdout/stderr interception, not method→level mapping).
• Fabric ↔ CLI (fabric/cluster-creation-management.md): pointer to harper login <Application URL> (introduced in Login cli #491) so new cluster users discover the CLI entry point; defers full CI/CD setup to the dedicated guide planned in Add a CI/CD deploy guide for Harper Fabric #502.
• Plugins listing (reference/components/overview.md): added @harperfast/vite-plugin to Known Custom Components; per the convention that plugins own their own docs, this is a link-out, not a duplicated page.

Closes

• Document JWT issuance via databases.system.hdb_user.operation #501 — JWT issuance from a Resource (rolled into this PR using server.operation)

Follow-ups (filed separately)

• Add a CI/CD deploy guide for Harper Fabric #502 — CI/CD deploy guide (two-script pattern, GH Actions template)
• Audit @harperdb vs @harperfast package namespace usage #503 — Audit @harperdb vs @harperfast namespace usage
• Recommend a canonical graphql.config.yml for Harper schemas #504 — Recommend a canonical graphql.config.yml
• @allow directive is parsed but not enforced harper#807 — @allow directive is parsed but not enforced; finish or remove
• vector-indexing rule: re-anchor must_cover to recover distance-threshold and $distance patterns skills#40 — re-anchor vector-indexing must_cover after this lands
• schema-design-tooling rule references nonexistent @auth directive — should be @allow skills#41 — fix nonexistent @auth directive reference
• logging rule: loggerWithTag is not a direct export from 'harper' skills#42 — fix loggerWithTag import (should be logger.withTag())

Test plan

• npm run format:check clean
• npm run typecheck clean
• npm run build succeeds with no broken links
• Spot-check rendered pages for layout and anchor targets (reviewer)

🤖 Drafted by Claude (Opus 4.7), on behalf of @kriszyp

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[Ethan-Arrowood]

When I merge this - we should see the cross-repo trigger happen 🤞

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