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Merge pull request #66 from Corvidae-Coding-Projects/agent/refactor-agent-system-remediation

Audit agent architecture and remove legacy rule injector

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.chainlink
- issues.db
- rules
- session.json
.claude
- OPENCLAUDIA.md
- hooks
- settings.json
.codex
- config.toml
.crosslink
- .gitignore
- driver-key.pub
- hook-config.json
- rules
.design
- acp-protocol-server.md
.github/workflows
- sandbox-security.yml
.gitignore
.mcp.json
.openclaudia
- config.yaml
- rules
  - global.md
AGENTS.md
ARCHITECTURE.md
CHANGELOG.md
CLAUDE.md
CLAUDE_CODE_FEATURES.md
COMPARISON.md
Cargo.lock
Cargo.toml
QA_REPORT.md
README.md
assets
- device_flow.html
capabilities
- automatic-learning-evaluation-corpus.json
- evaluation-corpus-review.json
- evaluation-corpus.json
- registry.json
- technical-memory-retrieval-evaluation.json
- technical-memory-retrieval-heldout.json
- technical-memory-retrieval-review.json
- technical-memory-retrieval-tuning.json
deny.toml
docs
- binary-capability-matrix.md
- claude-code-system-prompt-analysis.md
- designs
- evidence-based-coding-guardrails.md
- full-codebase-audit-2026-08-16.md
- historical-evidence
  - chainlink-history-v1.json
  - chainlink-retention-v1.json
- production-audit-problems.md
- production-remediation-design.md
- remediation-slices
- repository-artifact-dependency-policy.md
- sandbox-threat-model.md
- subprocess-inventory.md
examples
- generate_capability_matrix.rs
- generate_technical_memory_retrieval_evaluation.rs
fuzz
- .gitignore
- Cargo.lock
- Cargo.toml
- corpus
  - fuzz_anthropic_convert
    - seed-tool-roundtrip
  - fuzz_build_request
    - seed-provider-message
  - fuzz_cron_validate
    - seed-range-step
  - fuzz_hook_matcher
    - seed-exact-match
  - fuzz_json_tool_args
    - seed-classified-path
  - fuzz_path_resolve
    - seed-traversal
  - fuzz_safe_truncate
    - seed-unicode-boundary
  - fuzz_sse_event
    - seed-tool-sequence
  - fuzz_streaming_markdown
    - seed-fenced-unicode
- deny.toml
- fuzz_targets
- src
  - lib.rs
prompts/base
- comms.md
- identity.md
- principles.md
- tools.md
rust-toolchain.toml
sandbox-followups.md
scripts
- check_repository_hygiene.py
- export_legacy_chainlink.py
- tests
  - test_repository_policy.py
src
- acp.rs
- auto_learn.rs
- capability_evidence.rs
- claude_agent_sdk.rs
- claude_code_prompt.txt
- claude_credentials.rs
- cli
  - chat_repl.rs
  - commands
  - commit_pipeline.rs
  - display
  - print_mode.rs
  - repl
- codex_agent_sdk.rs
- codex_credentials.rs
- command_registry.rs
- compaction.rs
- config
  - acp.rs
  - environment.rs
  - guardrails.rs
  - hooks.rs
  - keybindings.rs
  - memory.rs
  - mod.rs
  - path_validation.rs
  - permissions.rs
  - provider.rs
  - proxy.rs
  - remote_actions.rs
  - session.rs
  - stop_conditions.rs
  - vdd.rs
  - webfetch.rs
- context.rs
- coordinator
  - mod.rs
  - permission.rs
  - planner.rs
  - tasks
    - local_shell.rs
  - teammate.rs
  - worker_lifecycle.rs
- decision.rs
- doctor.rs
- evidence.rs
- evidence_freshness.rs
- file_error.rs
- file_types.rs
- final_gate.rs
- git_transaction.rs
- grounded_loop.rs
- guardrails.rs
- hooks
  - claude_compat.rs
  - compat_import.rs
  - merge.rs
  - mod.rs
- keybindings
  - actions.rs
  - lookup.rs
  - mod.rs
  - parser.rs
  - resolver.rs
- ledger.rs
- lib.rs
- main.rs
- mcp.rs
- mcp_elicitation.rs
- mcp_inprocess.rs
- mcp_oauth.rs
- mcp_protocol.rs
- memdir
  - entrypoint.rs
  - mod.rs
- memory.rs
- memory
  - lesson.rs
  - portable.rs
  - record.rs
  - retrieval.rs
  - retrieval_evidence.rs
  - review.rs
  - source.rs
- migrations
  - ledger.rs
  - mod.rs
  - registry.rs
  - session_state_v1.rs
  - stamp_transcript_schema_v1.rs
  - tests.rs
- modes
  - fragments.rs
  - mod.rs
- oauth.rs
- output_style.rs
- permissions.rs
- permissions
  - receipts.rs
- persistence.rs
- persistence_windows.rs
- pipeline.rs
- plugins
  - activation.rs
  - install.rs
  - manager.rs
  - manifest.rs
  - marketplace.rs
  - mod.rs
  - policy.rs
  - transaction.rs
  - zip_cache.rs
- prompt.rs
- provider_budget.rs
- provider_credentials.rs
- provider_transport.rs
- providers
  - anthropic.rs
  - api_key.rs
  - deepseek.rs
  - google.rs
  - kimi.rs
  - minimax.rs
  - mod.rs
  - model_catalog.rs
  - ollama.rs
  - openai.rs
  - openai_compat.rs
  - qwen.rs
  - zai.rs
- proxy.rs
- rules.rs
- runtime
  - budget.rs
  - cancellation.rs
  - context.rs
  - event.rs
  - ids.rs
  - kernel.rs
  - mod.rs
  - provider_state.rs
  - reasoning.rs
  - reference.rs
  - side_question.rs
  - trace.rs
- secrets.rs
- services
  - analytics.rs
  - auto_compactor.rs
  - background.rs
  - feature_flags.rs
  - lifecycle.rs
  - lsp_diagnostics.rs
  - lsp_pool.rs
  - mcp_registry.rs
  - mod.rs
  - policy.rs
  - rate_limit_mock.rs
  - tool_executor.rs
- session
  - mod.rs
  - pricing.rs
  - state.rs
  - task.rs
- skills.rs
- skills
  - catalog.rs
  - trust.rs
- slash_commands.rs
- speculation
  - mod.rs
- state
  - categories.rs
  - causal.rs
  - local_events.rs
  - mod.rs
  - persist.rs
  - session.rs
  - store.rs
- subagent.rs
- task_graph.rs
- task_spec.rs
- team_memory.rs
- team_memory
  - authority.rs
  - replication.rs
  - transport.rs
- tool_intercept.rs
- tools
  - accumulator.rs
  - args.rs
  - ask_user.rs
  - bash
    - direct.rs
    - editor.rs
    - job.rs
    - kill.rs
    - mod.rs
    - output.rs
    - path_constraints.rs
    - path_lint.rs
    - policy.rs
    - sandbox.rs
  - catalog.rs
  - command.rs
  - continuation.rs
  - cron.rs
  - cron_scheduler.rs
  - crosslink.rs
  - effect.rs
  - file
    - discovery.rs
    - edit.rs
    - glob.rs
    - grep.rs
    - list.rs
    - mod.rs
    - notebook.rs
    - project_init.rs
    - read.rs
    - secure_fs.rs
    - secure_fs_windows.rs
    - workspace_projection.rs
    - write.rs
  - grounding.rs
  - host_safety.rs
  - lsp.rs
  - memory.rs
  - mod.rs
  - plan_mode.rs
  - registry.rs
  - remote_trigger.rs
  - result.rs
  - security.rs
  - skill.rs
  - task.rs
  - todo.rs
  - tool_search.rs
  - web.rs
  - worktree.rs
- transcript.rs
- tui
  - app.rs
  - components
    - help.rs
  - events.rs
  - input.rs
  - messages.rs
  - mod.rs
  - safety.rs
  - supervision.rs
- vdd
  - canonical.rs
  - engine.rs
  - error.rs
  - finalization.rs
  - helpers.rs
  - mod.rs
  - parsing.rs
  - prompts.rs
  - sink.rs
  - static_analysis.rs
  - transport.rs
  - triage.rs
- web.rs
- web_egress.rs
- web_supervisor.rs
- windows_fs.rs
tests
- analyze_with_hint_e2e.rs
- anthropic_builder_helpers_e2e.rs
- api_key_constructor_e2e.rs
- api_key_redaction_e2e.rs
- ask_user_question_validation_e2e.rs
- auto_compactor_e2e.rs
- auto_learn_preferences_e2e.rs
- automatic_learning_evaluation_e2e.rs
- background_agent_manager_e2e.rs
- bash_background_e2e.rs
- bash_dispatch_validation_e2e.rs
- bash_effect_classification_e2e.rs
- bash_integration.rs
- bash_output_kill_dispatch_e2e.rs
- bash_policy_validate_e2e.rs
- behavior_scope_targets_e2e.rs
- bounded_lsp_jsonrpc_e2e.rs
- canonical_typed_tool_results_e2e.rs
- capability_evidence_e2e.rs
- claude_compat_hooks_e2e.rs
- claude_credentials_auth_e2e.rs
- claude_credentials_constants_e2e.rs
- cli_exit_status_e2e.rs
- compact_boundary_helpers_e2e.rs
- compaction_constructors_e2e.rs
- compaction_estimator_e2e.rs
- config_guardrails_session_e2e.rs
- config_validation_e2e.rs
- context_injector_e2e.rs
- coordinator_permission_bridge_e2e.rs
- cron_dispatch_validation_e2e.rs
- cron_e2e.rs
- cron_schedule_shape_e2e.rs
- crosslink_dispatch_validation_e2e.rs
- descriptor_safe_persistence_e2e.rs
- edit_file_dispatch_validation_e2e.rs
- end_to_end_secret_redaction_e2e.rs
- evidence_bound_automatic_learning_e2e.rs
- execute_tool_envelope_e2e.rs
- extract_extensions_matrix_e2e.rs
- file_search_e2e.rs
- file_tools_integration.rs
- file_tools_race_e2e.rs
- fixtures
  - bounded_lsp_server.rs
  - mcp_echo_server.py
  - stateful_lsp_server.rs
- get_all_tool_definitions_subagents_e2e.rs
- get_context_window_table_e2e.rs
- glob_grep_dispatch_validation_e2e.rs
- google_anthropic_thinking_e2e.rs
- google_transform_request_envelope_e2e.rs
- grounding_context_dispatch_validation_e2e.rs
- hook_error_display_e2e.rs
- hooks_event_input_e2e.rs
- hooks_permissions_e2e.rs
- integration_tests.rs
- ledger_decision_e2e.rs
- legacy_rule_injector_removed_e2e.rs
- lifecycle_service_reachability_e2e.rs
- list_files_dispatch_validation_e2e.rs
- lsp_tool_validation_e2e.rs
- lsp_types_serde_e2e.rs
- mandatory_tool_effect_classification_e2e.rs
- mcp_http_transport_e2e.rs
- mcp_inprocess_transport_e2e.rs
- mcp_integration.rs
- mcp_manager_empty_e2e.rs
- mcp_registry_diagnostics_e2e.rs
- mcp_resource_handler_e2e.rs
- mcp_server_spec_from_plugin_config_e2e.rs
- mcp_types_shape_e2e.rs
- memdir_elicitation_e2e.rs
- memory_identity_e2e.rs
- migrations_runner_e2e.rs
- named_remote_action_runtime_e2e.rs
- non_bypassable_host_safety_e2e.rs
- notebook_edit_dispatch_validation_e2e.rs
- notebook_edit_e2e.rs
- oauth_pkce_flow_e2e.rs
- oauth_store_session_e2e.rs
- output_style_lifecycle_e2e.rs
- path_constraints_global_slot_e2e.rs
- path_validation_e2e.rs
- permission_check_auto_allow_e2e.rs
- permission_glob_match_semantics_e2e.rs
- permission_manager_tui_remember_e2e.rs
- permission_manager_unrestricted_e2e.rs
- permission_outcome_dispatch_e2e.rs
- permissions_mcp_tool_allowed_e2e.rs
- permissions_score_denial_e2e.rs
- pipeline_helpers_e2e.rs
- pipeline_integration.rs
- pipeline_resolve_headers_endpoint_e2e.rs
- plan_mode_exit_validation_e2e.rs
- plan_mode_policy_e2e.rs
- plugin_manifest_shapes_e2e.rs
- plugins_integration.rs
- progressive_tool_catalog_e2e.rs
- prompt_builder_e2e.rs
- prompt_legacy_builders_e2e.rs
- provider_dispatch_apikey_e2e.rs
- provider_dispatch_e2e.rs
- provider_headers_endpoint_matrix_e2e.rs
- provider_thinking_e2e.rs
- provider_transform_e2e.rs
- providers_e2e.rs
- proxy_config_defaults_e2e.rs
- read_file_dispatch_validation_e2e.rs
- registry_dispatch_envelope_e2e.rs
- registry_dispatch_options_e2e.rs
- registry_global_invariants_e2e.rs
- remote_trigger_mcp_e2e.rs
- repository_hook_import_e2e.rs
- rules_accessors_e2e.rs
- rules_context_e2e.rs
- rules_engine_deep_e2e.rs
- run_scoped_blast_radius_guardrails_e2e.rs
- runtime_kernel_e2e.rs
- runtime_mode_quiescence_e2e.rs
- sandbox_escape_e2e.rs
- service_registry_jobs_e2e.rs
- service_registry_lsp_pool_e2e.rs
- session_capability_isolation_e2e.rs
- session_compaction_e2e.rs
- session_context_plan_constants_e2e.rs
- session_filesystem_capabilities_e2e.rs
- skill_definition_aliases_e2e.rs
- skill_definition_frontmatter_e2e.rs
- skill_dispatch_validation_e2e.rs
- skill_execute_e2e.rs
- skill_trust_capabilities_e2e.rs
- stateful_lsp_service_e2e.rs
- subagent_config_result_shape_e2e.rs
- subagent_plan_mode_e2e.rs
- subagent_slash_e2e.rs
- support
  - mod.rs
- system_prompt_blocks_to_combined_e2e.rs
- task_dispatch_validation_e2e.rs
- task_manager_e2e.rs
- task_manager_format_e2e.rs
- task_status_display_serde_e2e.rs
- team_memory_authority_cli_e2e.rs
- team_memory_authority_e2e.rs
- team_memory_replication_e2e.rs
- team_memory_thinking_e2e.rs
- technical_memory_conflict_resolution_e2e.rs
- technical_memory_e2e.rs
- technical_memory_portable_e2e.rs
- technical_memory_retrieval_e2e.rs
- technical_memory_retrieval_evidence_e2e.rs
- technical_memory_review_e2e.rs
- technical_memory_source_e2e.rs
- thinking_budget_provider_config_e2e.rs
- todo_session_isolation_e2e.rs
- todo_write_dispatch_validation_e2e.rs
- tool_context_dispatch_e2e.rs
- tool_control_signal_e2e.rs
- tool_intercept_buffer_e2e.rs
- tool_registry_handler_e2e.rs
- tool_registry_schema_e2e.rs
- tool_search_dispatch_e2e.rs
- tools_e2e.rs
- tools_security_e2e.rs
- transcript_path_helpers_e2e.rs
- transform_request_per_provider_e2e.rs
- typed_environment_config_e2e.rs
- validate_base_url_security_e2e.rs
- vdd_subconfig_defaults_e2e.rs
- vdd_triage_e2e.rs
- web_fetch_config_e2e.rs
- web_integration.rs
- web_ssrf_e2e.rs
- web_tool_url_validation_e2e.rs
- webhook_endpoint_shape_e2e.rs
- webhook_error_display_e2e.rs
- webhook_registry_lifecycle_e2e.rs
- webhook_validate_url_e2e.rs
- worktree_dispatch_validation_e2e.rs
- worktree_lsp_e2e.rs
- wrap_system_reminder_deeper_e2e.rs
- write_file_dispatch_validation_e2e.rs

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