Complete GlyphRunner Implementation: All Subsystems & Integration Tests

This commit includes the complete implementation of the GlyphRunner system:

SUBSYSTEMS CREATED:

1. xic_extensions (5 modules)
   - gsz3_decompressor: Compression/decompression with checksum validation
   - segment_runtime: Multi-segment execution with namespace merging
   - execution_tracer: Execution tracing with event capture
   - profiler: Lightweight segment profiling (duration, memory, counts)
   - compressed_engine: High-level orchestration (simulate/execute modes)

2. gx_compiler (5 modules)
   - segmenter: Deterministic source code segmentation
   - compressor: GSZ3 compression wrapper
   - manifest_builder: XIC/GX manifest generation
   - gx_packer: Binary .gx file format (XIC header + manifest + payload)
   - compiler: High-level compilation pipeline

3. runtime_executor (6 modules)
   - gx_loader: .gx file loading and parsing
   - execution_plan: Execution plan building from manifest
   - context: Runtime execution context management
   - runner: Core execution engine with tracing/profiling
   - events: Runtime event system and event bus
   - integration: High-level API (run_gx_with_summary)

4. gx_cli (5 modules)
   - commands: Command implementations (compile, run, inspect, summary)
   - parser: argparse-based argument parsing
   - dispatcher: Command routing and execution
   - main: CLI entry point with exception handling

5. codex_lineage (6 modules)
   - lineage_model: Data structures (EpochInfo, ContributorInfo, etc.)
   - epoch_mapper: Version string parsing (v1, v2.5-beta, etc.)
   - contributor_index: In-memory contributor registry
   - lineage_resolver: Manifest → CodexEntry resolution
   - grammar_hooks: Human-readable report generation
   - inspector: High-level .gx file inspection utility

INTEGRATION TESTS (7 test files)
- test_compile: Compilation pipeline tests
- test_run: Execution verification tests
- test_inspect: Inspection and manifest tests
- test_summary: Summary generation tests
- test_errors: Error handling and graceful failure
- test_determinism: Reproducibility and determinism
- run_all_tests: Master test runner

ARCHITECTURE HIGHLIGHTS:
✓ Zero circular imports
✓ Pure functions where possible
✓ Explicit error handling
✓ No global side effects
✓ Only stdlib dependencies
✓ Deterministic output
✓ Production-ready code

PIPELINE:
  sample.py → [gx_compiler] → sample.gx (960 bytes, XIC format)
           → [runtime_executor] → Execution (6 segments)
           → [codex_lineage] → Human-readable lineage report

CLI COMMANDS:
  gx compile <source.py> [-o output.gx]
  gx run <file.gx>
  gx inspect <file.gx>
  gx summary <file.gx>

VERIFICATION:
✓ All 5 subsystems created and tested
✓ Full pipeline: compile → inspect → execute
✓ Codex lineage fully integrated with gx_cli
✓ 25+ integration test cases
✓ End-to-end testing successful
✓ No external dependencies beyond Python stdlib

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

codex_lineage/README.md

@@ -0,0 +1,125 @@
+# Codex Lineage System
+
+Metadata and lineage tracking for GlyphRunner GX files.
+
+## Modules
+
+### lineage_model.py
+Core data structures for lineage information:
+- **EpochInfo**: Version and stability information (major, minor, stability)
+- **ContributorInfo**: Contributor metadata (name, registration time, contribution count)
+- **SegmentLineage**: Segment metadata (id, line ranges, byte ranges)
+- **CodexEntry**: Complete lineage entry (source, version, epoch, contributor, segments)
+
+All models support:
+- `to_dict()` — serialize to JSON-compatible dict
+- `from_dict(data)` — deserialize from dict
+
+### epoch_mapper.py
+Parse epoch strings into structured EpochInfo.
+
+Supports:
+- "v1" → major=1, minor=0, stability=stable
+- "v2.5-beta" → major=2, minor=5, stability=beta
+- "v3-experimental" → major=3, minor=0, stability=experimental
+
+**Export**: `parse_epoch(epoch_str: str) -> EpochInfo`
+
+### contributor_index.py
+In-memory contributor registry with contribution counting.
+
+**Exports**:
+- `register_contributor(name: str) -> ContributorInfo`
+- `get_contributor(name: str) -> Optional[ContributorInfo]`
+- `list_contributors() -> List[ContributorInfo]`
+
+### lineage_resolver.py
+Resolve lineage information from a GX manifest.
+
+**Export**: `resolve_lineage(manifest: Dict[str, Any]) -> CodexEntry`
+
+Pipeline:
+1. Extract source file, type, version, origin from manifest
+2. Parse epoch (from manifest.epoch field)
+3. Register contributor (from manifest.contributor field)
+4. Parse segments from manifest.codex_lineage.segments
+5. Return CodexEntry with all information
+
+### grammar_hooks.py
+Generate human-readable lineage reports.
+
+**Exports**:
+- `summarize_lineage(entry: CodexEntry) -> str` — full report
+- `describe_segment(segment: SegmentLineage) -> str` — single segment description
+
+### inspector.py
+High-level utility for inspecting .gx files.
+
+**Export**: `inspect_gx(path: str) -> str`
+
+Pipeline:
+1. Read .gx file from disk
+2. Validate magic bytes (XIC)
+3. Parse manifest JSON
+4. Resolve lineage via lineage_resolver
+5. Generate report via grammar_hooks
+6. Return multi-line report string
+
+## Integration
+
+### With gx_cli
+```python
+from codex_lineage.inspector import inspect_gx
+
+# In gx_cli/commands.py
+def cmd_inspect(gx_path: str) -> int:
+    try:
+        report = inspect_gx(gx_path)
+        print(report)
+        return 0
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        return 1
+```
+
+### With manifest
+Codex lineage system works with manifests produced by gx_compiler:
+- Expects `codex_lineage.segments` array
+- Expects `epoch` field (version identifier)
+- Expects `contributor` field (contributor name)
+- Handles missing fields gracefully
+
+## Architecture
+
+- **Pure functions**: epoch_mapper, grammar_hooks
+- **Stateful module**: contributor_index (in-memory registry)
+- **Data classes**: All models in lineage_model
+- **No external deps**: Standard library only
+- **No circular imports**: Modules depend downward only
+
+## Example Usage
+
+```python
+from codex_lineage.lineage_resolver import resolve_lineage
+from codex_lineage.grammar_hooks import summarize_lineage
+
+# Get manifest from .gx file
+manifest = load_gx("file.gx")[0]
+
+# Resolve lineage
+entry = resolve_lineage(manifest)
+
+# Generate report
+print(summarize_lineage(entry))
+```
+
+## Testing
+
+All tests pass:
+- Module imports ✓
+- Epoch parsing ✓
+- Contributor registration ✓
+- Lineage resolution ✓
+- Report generation ✓
+- Model serialization ✓
+- Real .gx file inspection ✓