Add missing examples, fix documentation, and improve tooling

CHANGELOG.md

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+# Changelog
+
+All notable changes to the Codex file format specification.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+## [Unreleased]
+
+### Added
+- Legal extension example document (`examples/legal-document/`)
+- Precise layout example (`examples/presentation-document/presentation/layouts/letter.json`)
+- Highlight annotation documentation in collaboration extension (Section 4.7)
+- Example coverage checking capability in sync checker
+
+### Fixed
+- Broken cross-reference in presentation layers spec (Section 5.1.2 → 5.4)
+- Sync checker false positives for MIME types, token types, and enum values
+
+### Changed
+- Content schema now references legal extension marks (`legal:cite`)
+
+## [0.1] - 2025-01 (Draft)
+
+### Added
+
+#### Core Specification
+- Document manifest with state machine (draft → review → frozen → published)
+- Content block model with 22 block types
+- Dublin Core metadata support
+- Asset embedding and management
+- Provenance and lineage tracking
+- Anchors and references system
+- Presentation layers (paginated, continuous, responsive, precise)
+
+#### Extensions
+- **Academic** (`codex.academic`) - Theorems, proofs, exercises, algorithms, equation groups
+- **Collaboration** (`codex.collaboration` v0.2) - CRDT integration, comments, change tracking, presence
+- **Forms** (`codex.forms`) - Interactive form fields with validation
+- **Legal** (`codex.legal`) - Citations, Table of Authorities, court captions, signature blocks
+- **Phantoms** (`codex.phantoms`) - Invisible structural elements for complex layouts
+- **Presentation** (`codex.presentation`) - Advanced typography, master pages, print features
+- **Security** (`codex.security`) - Digital signatures, encryption, redaction, scoped signatures
+- **Semantic** (`codex.semantic`) - Bibliography, footnotes, glossary, entity markup, JSON-LD
+
+#### Profiles
+- Simple Documents profile for recreational reading
+
+#### Tooling
+- JSON Schema validation for all specification components
+- Example document validation
+- Cross-reference validation
+- Spec-schema synchronization checking
+- Template generation script
+
+### Notes
+- This is an initial draft specification
+- The collaboration extension migrated from v0.1 to v0.2 (anchor-based addressing)
+- Feedback welcome via GitHub issues

examples/legal-document/content/document.json

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+{
+  "version": "0.1",
+  "blocks": [
+    {
+      "type": "legal:caption",
+      "id": "caption",
+      "court": "United States District Court for the Northern District of California",
+      "caseNumber": "No. 3:24-cv-01234",
+      "parties": {
+        "plaintiff": "Jane Doe",
+        "defendant": "Acme Corporation"
+      },
+      "docket": "Hon. Sarah Johnson"
+    },
+    {
+      "type": "heading",
+      "id": "doc-title",
+      "level": 1,
+      "children": [
+        { "type": "text", "value": "Brief in Support of Motion for Summary Judgment" }
+      ]
+    },
+    {
+      "type": "legal:tableOfAuthorities",
+      "id": "toa",
+      "title": "Table of Authorities",
+      "categories": [
+        { "name": "Cases", "key": "cases", "format": "bluebook" },
+        { "name": "Statutes", "key": "statutes", "format": "bluebook" },
+        { "name": "Regulations", "key": "regulations", "format": "bluebook" }
+      ],
+      "pageReferences": true,
+      "passimThreshold": 5
+    },
+    {
+      "type": "heading",
+      "id": "intro-heading",
+      "level": 2,
+      "children": [
+        { "type": "text", "value": "I. Introduction" }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "intro-para-1",
+      "children": [
+        { "type": "text", "value": "Plaintiff Jane Doe respectfully submits this brief in support of her Motion for Summary Judgment. As demonstrated below, the undisputed facts establish that Defendant violated " },
+        {
+          "type": "text",
+          "value": "Title VII of the Civil Rights Act of 1964",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "42 U.S.C. \u00a7 2000e et seq.",
+              "category": "statutes"
+            }
+          ]
+        },
+        { "type": "text", "value": " by terminating Plaintiff's employment based on her gender." }
+      ]
+    },
+    {
+      "type": "heading",
+      "id": "facts-heading",
+      "level": 2,
+      "children": [
+        { "type": "text", "value": "II. Statement of Undisputed Facts" }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "facts-para-1",
+      "children": [
+        { "type": "text", "value": "Plaintiff was employed by Defendant from January 2020 until her termination on June 15, 2024. During her employment, Plaintiff received consistently positive performance reviews and was promoted twice." }
+      ]
+    },
+    {
+      "type": "heading",
+      "id": "argument-heading",
+      "level": 2,
+      "children": [
+        { "type": "text", "value": "III. Argument" }
+      ]
+    },
+    {
+      "type": "heading",
+      "id": "argument-a-heading",
+      "level": 3,
+      "children": [
+        { "type": "text", "value": "A. Standard of Review" }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "standard-para-1",
+      "children": [
+        { "type": "text", "value": "Summary judgment is appropriate when there is no genuine dispute as to any material fact and the movant is entitled to judgment as a matter of law. " },
+        {
+          "type": "text",
+          "value": "Celotex Corp. v. Catrett",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "477 U.S. 317 (1986)",
+              "category": "cases",
+              "shortForm": "Celotex"
+            }
+          ]
+        },
+        { "type": "text", "value": ". The moving party bears the initial burden of demonstrating the absence of a genuine issue of material fact. " },
+        {
+          "type": "text",
+          "value": "Id.",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "477 U.S. 317 (1986)",
+              "category": "cases",
+              "shortForm": "Celotex",
+              "pinpoint": "at 323"
+            }
+          ]
+        },
+        { "type": "text", "value": "" }
+      ]
+    },
+    {
+      "type": "heading",
+      "id": "argument-b-heading",
+      "level": 3,
+      "children": [
+        { "type": "text", "value": "B. Plaintiff Has Established a Prima Facie Case of Discrimination" }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "prima-facie-para-1",
+      "children": [
+        { "type": "text", "value": "Under the burden-shifting framework established in " },
+        {
+          "type": "text",
+          "value": "McDonnell Douglas Corp. v. Green",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "411 U.S. 792 (1973)",
+              "category": "cases",
+              "shortForm": "McDonnell Douglas"
+            }
+          ]
+        },
+        { "type": "text", "value": ", a plaintiff establishes a prima facie case of discrimination by showing: (1) membership in a protected class; (2) satisfactory job performance; (3) an adverse employment action; and (4) circumstances giving rise to an inference of discrimination." }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "prima-facie-para-2",
+      "children": [
+        { "type": "text", "value": "The Ninth Circuit has consistently applied this framework. See " },
+        {
+          "type": "text",
+          "value": "Chuang v. Univ. of Cal. Davis",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "225 F.3d 1115, 1123 (9th Cir. 2000)",
+              "category": "cases",
+              "shortForm": "Chuang"
+            }
+          ]
+        },
+        { "type": "text", "value": ". Furthermore, EEOC regulations provide that employers must maintain records of employment decisions. " },
+        {
+          "type": "text",
+          "value": "29 C.F.R. \u00a7 1602.14",
+          "marks": [
+            {
+              "type": "legal:cite",
+              "citation": "29 C.F.R. \u00a7 1602.14",
+              "category": "regulations"
+            }
+          ]
+        },
+        { "type": "text", "value": "." }
+      ]
+    },
+    {
+      "type": "heading",
+      "id": "conclusion-heading",
+      "level": 2,
+      "children": [
+        { "type": "text", "value": "IV. Conclusion" }
+      ]
+    },
+    {
+      "type": "paragraph",
+      "id": "conclusion-para-1",
+      "children": [
+        { "type": "text", "value": "For the foregoing reasons, Plaintiff respectfully requests that this Court grant summary judgment in her favor on her Title VII claim." }
+      ]
+    },
+    {
+      "type": "legal:signatureBlock",
+      "id": "sig-block",
+      "role": "counsel",
+      "signer": {
+        "name": "Jane Smith",
+        "title": "Counsel for Plaintiff",
+        "barNumber": "CA 123456",
+        "firm": "Smith & Associates LLP",
+        "address": "100 Market Street, Suite 500, San Francisco, CA 94105",
+        "telephone": "(415) 555-1234",
+        "email": "jsmith@smithlaw.com"
+      },
+      "date": "2025-01-30"
+    }
+  ]
+}

examples/legal-document/manifest.json

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+{
+  "codex": "0.1",
+  "id": "pending",
+  "state": "draft",
+  "created": "2025-01-30T10:00:00Z",
+  "modified": "2025-01-30T10:00:00Z",
+  "extensions": [
+    {
+      "id": "codex.legal",
+      "version": "0.1",
+      "required": false
+    }
+  ],
+  "content": {
+    "path": "content/document.json",
+    "hash": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
+  },
+  "metadata": {
+    "dublinCore": "metadata/dublin-core.json"
+  },
+  "legal": {
+    "citationStyle": "bluebook",
+    "jurisdiction": "US"
+  }
+}

examples/legal-document/metadata/dublin-core.json

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+{
+  "version": "1.1",
+  "terms": {
+    "title": "Brief in Support of Motion for Summary Judgment",
+    "creator": ["Jane Smith, Esq."],
+    "subject": ["civil rights", "employment discrimination"],
+    "description": "A demonstration of the legal extension features including caption, Table of Authorities, legal citations, and signature block.",
+    "date": "2025-01-30",
+    "type": "Text",
+    "format": "application/vnd.codex+zip",
+    "language": "en",
+    "rights": "Confidential - Attorney Work Product"
+  }
+}