feat(lint): add machine fixes

[pocky]

Summary

• Add CAS-guarded workspace/applyEdits support so sidecar extensions can request safe, host-owned text mutations with dry-run previews and conflict reporting.
• Extend the lint extension with tower_lint_fix, including structured fix extraction, dry-run/apply behavior, skip reasons, and stable tool error responses.
• Wire apply-edits through daemon state, extension discovery, sidecar dispatch, and extension event delivery while avoiding reentrant file-change deadlocks.
• Document lint fix usage and update project memory for the F003 implementation and review rules.

Changes

Project Memory

• .zpm/kb/feedback/journal.wal: Add F003 review, testing, protocol, and apply-edits architecture rules.
• .zpm/kb/pr_feature_f003_lint_fix_apply_machine_applicable_lin/journal.wal: Add PR tracking journal entries for resolved implementation scan items.
• .zpm/kb/pr_feature_f003_lint_fix_apply_machine_applicable_lin/knowledge.pl: Add PR tracking schema and readiness predicates for this branch.
• .zpm/mounts.json: Mount the F003 PR memory segment.

Core Apply-Edits Domain

• crates/core_engine/src/domain/error.rs: Add UnsupportedOperation for unavailable public contracts.
• crates/core_engine/src/domain/mutation/file_mutation.rs: Implement CAS and dry-run multi-edit application with UTF-8 validation, conflict filtering, previews, and indexed commits.
• crates/core_engine/src/domain/mutation/mod.rs: Register apply-edits domain tests.
• crates/core_engine/src/domain/mutation/apply_edits_tests.rs: Add focused tests for contracts, CAS rejection, dry-run previews, conflicts, UTF-8 boundaries, and commit behavior.
• crates/core_engine/src/ports/inbound.rs: Add apply-edits DTOs and FileMutationUseCase methods.

Extension Host Wiring

• crates/core_engine/src/adapters/daemon/engine.rs: Wire EngineApplyEditsHost into daemon state and defer extension notifications until locks are released.
• crates/core_engine/src/adapters/extension/discovery.rs: Add shared-registry loading so eager extensions can use host calls during initialization.
• crates/core_engine/src/adapters/extension/host_deps.rs: Add ApplyEditsHostPort and unsupported fallback dependency.
• crates/core_engine/src/adapters/extension/mod.rs: Export new extension discovery helpers.
• crates/core_engine/src/adapters/extension/sidecar.rs: Dispatch workspace/applyEdits, validate params, enforce capability declaration, and map CAS/range errors.
• crates/core_engine/src/adapters/extension/supervisor.rs: Clone the apply-edits dependency during respawn.
• crates/core_engine/src/domain/extension_host/mod.rs: Queue deferred events when an extension instance is busy to avoid reentrant deadlocks.
• crates/core_engine/src/adapters/mcp/native_tools.rs: Expose the current extension host from engine state.

Lint Fix Extension

• extensions/lint/extension.toml: Declare the fix tool and request_apply_edits capability.
• extensions/lint/src/fixes.rs: Add lint fix model types.
• extensions/lint/src/lib.rs: Export fix support.
• extensions/lint/src/main.rs: Add fix orchestration, CAS hashing, dry-run handling, apply-edits host calls, and structured tool results.
• extensions/lint/src/parsers.rs: Extract structured fixes from supported linter output formats.
• extensions/lint/src/protocol.rs: Add fix request/result DTOs, preview DTOs, skip reasons, and stable error response types.
• extensions/lint/src/runner.rs: Preserve fix metadata through linter execution.
• extensions/lint/tests/protocol_tests.rs: Cover lint fix protocol serialization and manifest behavior.

Tests

• crates/core_engine/src/adapters/extension/supervisor_tests.rs: Add apply-edits fallback dependency to host fixture setup.
• crates/core_engine/src/adapters/extension/tests.rs: Add apply-edits fallback dependency to sidecar tests.
• crates/core_engine/tests/extension_ast_e2e.rs: Add apply-edits fallback dependency to AST extension fixtures.
• crates/core_engine/tests/extension_fmt_e2e.rs: Add apply-edits fallback dependency to formatting extension fixtures.
• crates/core_engine/tests/extension_lint_e2e.rs: Add apply-edits runtime, reentrancy, manifest, protocol, parser, dry-run, conflict, and lint fix orchestration coverage.
• crates/core_engine/tests/extension_lsp_process_e2e.rs: Add apply-edits fallback dependency to LSP process fixtures.
• crates/core_engine/tests/extension_lsp_protocol_e2e.rs: Add apply-edits fallback dependency to LSP protocol fixtures.
• crates/core_engine/tests/functional_lint_fix_mcp.rs: Add MCP-level lint fix coverage.
• crates/core_engine/tests/functional_lint_mcp.rs: Update lint MCP expectations for the added fix capability/tool surface.
• crates/core_engine/tests/lint_support.rs: Add lint fix manifests, apply-edits-capable test host dependencies, and fixture helpers.
• crates/extension_protocol/tests/protocol_tests.rs: Add protocol tests for request-apply-edits host calls and manifest capability stability.

Protocol

• crates/extension_protocol/src/manifest.rs: Add request_apply_edits capability support.
• crates/extension_protocol/src/messages.rs: Add RequestApplyEdits host call wire DTOs.

Documentation

• README.md: Describe lint fixes and add a dry-run example.
• docs/README.md: Link lint fix user documentation.
• docs/architecture.md: Document apply-edits flow in the host architecture.
• docs/extensions.md: Document the request_apply_edits capability for extensions.
• docs/getting-started.md: Add lint fix usage to onboarding flow.
• docs/mcp-tools.md: Document tower_lint_fix, arguments, results, and errors.
• docs/user-guide/lint-fixes.md: Add user guide for previewing and applying structured lint fixes safely.

Test plan

• Run cargo fmt --check
• Run cargo clippy --workspace --all-targets -- -D warnings
• Run cargo build --workspace --bins
• Run cargo test --workspace

Closes #6

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