feat(semantic): add symbol edit tools

[pocky]

Summary

• Add semantic symbol editing across MCP, AST, and LSP surfaces so callers can resolve symbols, preview edits, and apply rename/body/signature changes through structured contracts.
• Introduce batch workspace edit application with CAS/base-hash validation to keep multi-file edits atomic and conflict-aware.
• Extend extension protocol, host dependencies, and daemon wiring so sidecar extensions can request workspace reads, apply edits, and expose semantic edit tools.
• Document the new semantic edit workflows and update tests across protocol, domain, extension, and functional MCP coverage.

Changes

Workspace Metadata

• .zpm/kb/architecture/journal.wal: Record architecture knowledge discovered during semantic edit implementation.
• .zpm/kb/feedback/journal.wal: Record feedback rules and implementation lessons from the semantic edit work.
• Cargo.lock: Update dependency lockfile for workspace changes.

Core Engine

• crates/core_engine/src/adapters/daemon/engine.rs: Wire semantic edit capabilities through the daemon/MCP engine.
• crates/core_engine/src/adapters/extension/host_deps.rs: Extend sidecar host dependencies with workspace edit/read support.
• crates/core_engine/src/adapters/extension/sidecar.rs: Add host-call plumbing for semantic edit operations.
• crates/core_engine/src/adapters/extension/tests.rs: Cover extension host dependency and sidecar behavior for the new edit flows.
• crates/core_engine/src/adapters/in_memory_code_intel.rs: Update in-memory code intelligence support for semantic navigation/edit tests.
• crates/core_engine/src/domain/grep/mod.rs: Adjust grep/domain integration used by indexed symbol workflows.
• crates/core_engine/src/domain/mutation/file_mutation.rs: Add batch workspace apply-edits behavior with validation and structured results.
• crates/core_engine/src/ports/inbound.rs: Extend inbound use-case contracts for semantic edit operations.
• crates/core_engine/src/ports/mod.rs: Export updated port modules.
• crates/core_engine/src/ports/navigation.rs: Add navigation/edit contract types for implementation and rename flows.
• crates/core_engine/src/test_support/mod.rs: Add shared fixtures and helpers for semantic edit testing.

Core Engine Tests

• crates/core_engine/src/domain/mutation/apply_edits_tests.rs: Add contract coverage for batch edit application, conflicts, and validation.
• crates/core_engine/tests/extension_ast_e2e.rs: Add AST sidecar end-to-end coverage for anchored symbol edits.
• crates/core_engine/tests/extension_lint_e2e.rs: Update lint extension test support after protocol/host dependency changes.
• crates/core_engine/tests/extension_lsp_process_e2e.rs: Cover LSP sidecar process behavior for semantic navigation/edit handlers.
• crates/core_engine/tests/extension_lsp_protocol_e2e.rs: Cover LSP protocol responses for implementation and rename operations.
• crates/core_engine/tests/functional_semantic_edit_mcp.rs: Add functional MCP tests for semantic edit tool responses.
• crates/core_engine/tests/lint_support.rs: Update shared lint test fixtures for extension protocol changes.

Extension Protocol

• crates/extension_protocol/src/lib.rs: Export semantic edit protocol types.
• crates/extension_protocol/src/messages.rs: Add JSON-RPC message contracts for workspace edits, implementation lookup, prepare rename, and rename.
• crates/extension_protocol/tests/semantic_edit_contracts.rs: Add protocol contract tests for semantic edit serialization and error payloads.

AST Extension

• extensions/ast/Cargo.toml: Update AST extension dependencies for anchored edit support.
• extensions/ast/extension.toml: Declare AST semantic edit tools and capabilities.
• extensions/ast/src/index.rs: Update symbol indexing support used by edit resolution.
• extensions/ast/src/main.rs: Register anchored symbol edit handlers.
• extensions/ast/src/outline.rs: Extend outline parsing for edit anchor resolution.
• extensions/ast/src/protocol.rs: Add AST extension request/response types for semantic edit tools.
• extensions/ast/src/symbols.rs: Resolve symbol spans from current file content for safe anchored edits.
• extensions/ast/src/tools.rs: Implement AST semantic edit tools, dry-run previews, content hashes, and structured errors.

LSP Extension

• extensions/lsp/Cargo.toml: Update LSP extension dependencies for workspace edit decoding and semantic navigation.
• extensions/lsp/extension.toml: Declare LSP implementation and rename tools.
• extensions/lsp/src/lsp_adapter/decode.rs: Decode LSP workspace edits, including versioned document changes, into core edit operations.
• extensions/lsp/src/lsp_adapter/mod.rs: Add adapter operations for implementation lookup, prepare rename, and rename.
• extensions/lsp/src/lsp_adapter/pool.rs: Extend session pool routing for new LSP operations.
• extensions/lsp/src/lsp_adapter/position_map.rs: Convert UTF-16 LSP ranges to byte ranges for workspace edits.
• extensions/lsp/src/main.rs: Register LSP semantic edit and navigation handlers.
• extensions/lsp/src/protocol.rs: Add request/response protocol types for implementation and rename tools.
• extensions/lsp/src/session.rs: Add session-level handling for implementation and rename requests.
• extensions/lsp/src/tools.rs: Implement MCP-facing LSP tools for implementation lookup, prepare rename, and rename.

Documentation

• README.md: Update project feature overview with semantic edit support.
• docs/README.md: Link semantic edit documentation from the docs index.
• docs/architecture.md: Document architecture changes for semantic edit routing across ports and extensions.
• docs/extensions.md: Document extension capabilities and host-call expectations for semantic edits.
• docs/mcp-tools.md: Document MCP tool surface changes for AST/LSP semantic edit workflows.
• docs/user-guide/semantic-edits.md: Add user guide for semantic symbol editing workflows.

Test plan

• Run formatting: cargo fmt --check
• Run linting: cargo clippy --workspace --all-targets -- -D warnings
• Build sidecar binaries: cargo build --workspace --bins
• Run full test suite: cargo test --workspace

Closes #14

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