Change arch (#156)

* Improve coverage and clean up tests

* Fix formatter protocol contract

* Refine reporter structure and adapter naming

* improve report component

* improve report component

* remove backward compatibility shims

* fix tests after removing compatibility shims

* polish docs and main import

* document sandbox provider return types

* add auth loader coverage tests

Author: Agent-Hellboy

README.md

@@ -51,7 +51,105 @@ It does **not** use instrumentation-based fuzzing (no coverage or binary/source
 
 ### Basic Fuzzer Flow
 
-![Basic fuzzer flow diagram](images/fuzzer-flow.svg)
+```mermaid
+flowchart TB
+    subgraph CLI["CLI + Config"]
+        A1[parse_arguments]
+        A2[ValidationManager]
+        A3[build_cli_config]
+        A4[ClientSettings]
+        A1 --> A2 --> A3 --> A4
+    end
+
+    subgraph Runtime["Runtime Orchestration"]
+        B1[run_with_retry_on_interrupt]
+        B2[unified_client_main]
+        B3[RunPlan + Commands]
+        B4[ClientExecutionPipeline]
+        B1 --> B2 --> B3 --> B4
+    end
+
+    subgraph Transport["Transport Layer"]
+        C1[DriverCatalog + build_driver]
+        C2[TransportDriver]
+        C3[HttpDriver / SseDriver / StdioDriver / StreamHttpDriver]
+        C4[JsonRpcAdapter]
+        C5[RetryingTransport (optional)]
+        C1 --> C2 --> C3
+        C3 --> C4
+        C3 --> C5
+    end
+
+    subgraph Clients["Client Layer"]
+        D1[MCPFuzzerClient]
+        D2[ToolClient]
+        D3[ProtocolClient]
+        D1 --> D2
+        D1 --> D3
+    end
+
+    subgraph Mutators["Mutators + Strategies"]
+        E1[ToolMutator]
+        E2[ProtocolMutator]
+        E3[ToolStrategies / ProtocolStrategies]
+        E4[SeedPool + mutate_seed_payload]
+        E1 --> E3
+        E2 --> E3
+        E1 --> E4
+        E2 --> E4
+    end
+
+    subgraph Execution["Execution + Concurrency"]
+        F1[AsyncFuzzExecutor]
+        F2[ToolExecutor]
+        F3[ProtocolExecutor]
+        F4[ResultBuilder]
+        F1 --> F2
+        F1 --> F3
+        F2 --> F4
+        F3 --> F4
+    end
+
+    subgraph Safety["Safety System"]
+        G1[SafetyFilter + DangerDetector]
+        G2[Filesystem Sandbox]
+        G3[System Command Blocker]
+        G4[Network Policy]
+        G1 --> G2
+        G1 --> G3
+        G1 --> G4
+    end
+
+    subgraph RuntimeMgr["Process Runtime"]
+        H1[ProcessManager]
+        H2[ProcessWatchdog]
+        H3[SignalDispatcher]
+        H4[ProcessSupervisor]
+        H1 --> H2
+        H1 --> H3
+        H4 --> H1
+    end
+
+    subgraph Reporting["Reporting + Output"]
+        I1[FuzzerReporter]
+        I2[FormatterRegistry]
+        I3[OutputProtocol + OutputManager]
+        I4[Console/JSON/CSV/XML/HTML/MD Formatters]
+        I1 --> I2 --> I4
+        I1 --> I3
+    end
+
+    A4 --> B1
+    B4 --> D1
+    C1 --> D1
+    D2 --> E1
+    D3 --> E2
+    E1 --> F2
+    E2 --> F3
+    D1 --> G1
+    C3 --> H4
+    D1 --> I1
+```
 
 ### Extensibility for Contributors
 MCP Server Fuzzer is designed for easy extension while keeping CLI usage simple:

docs/architecture/architecture.md

@@ -25,7 +25,7 @@ flowchart TB
   end
 
   subgraph Client
-    B1[UnifiedMCPFuzzerClient (client/main.py)]
+    B1[MCPFuzzerClient (client/main.py)]
     B2[Safety Integration]
     B3[Reporting Integration]
   end

docs/components/process-management.md

@@ -36,10 +36,10 @@ The executor's concurrency can be configured in several ways:
    executor = AsyncFuzzExecutor(max_concurrency=10)
    ```
 
-2. **Via UnifiedMCPFuzzerClient**:
+2. **Via MCPFuzzerClient**:
 
    ```python
-   client = UnifiedMCPFuzzerClient(
+   client = MCPFuzzerClient(
        transport,
        max_concurrency=10  # Controls concurrency for both tool and protocol fuzzers
    )
@@ -174,6 +174,20 @@ async def main():
 asyncio.run(main())
 ```
 
+### ProcessManager Lifecycle States
+
+| Stage | Trigger | Notes |
+| --- | --- | --- |
+| Unregistered | Initial state | Process not tracked by registry. |
+| Registered | `register_existing_process` | Process added to registry and watchdog. |
+| Running | `start_process` | Process launched and `started` event emitted. |
+| Stopping | `stop_process` | Graceful/forced stop requested. |
+| Stopped | `stop_process` / exit | Process stopped, `stopped` event emitted. |
+| Shutdown | `shutdown` | All processes stopped, watchdog stopped, registry cleared. |
+
+Events emitted by the manager (`started`, `stopped`, `stopped_all`, `shutdown`,
+`shutdown_failed`, `signal`, `signal_all`) allow observers to track transitions.
+
 ## Configuration
 
 ### WatchdogConfig

docs/components/safety.md

@@ -160,6 +160,51 @@ it to a bug report or CI artifact. Standardized output artifacts (`output.types`
 containing `safety_summary`) convey the same information in a machine-readable
 format.
 
+## Extending Detection and Sandbox Providers
+
+You can customize detection patterns by passing explicit lists when constructing
+`SafetyFilter`:
+
+```python
+from mcp_fuzzer.safety_system.safety import SafetyFilter
+
+custom_filter = SafetyFilter(
+    dangerous_url_patterns=[r"https?://", r"example\\.com"],
+    dangerous_script_patterns=[r"<script", r"onload="],
+    dangerous_command_patterns=[r"rm\\s+-rf", r"shutdown"],
+    dangerous_argument_names=["path", "command"],
+)
+```
+
+To swap the filesystem sandbox implementation, implement the `SandboxProvider`
+protocol and pass it to `SafetyFilter`:
+
+```python
+from mcp_fuzzer.safety_system.safety import SandboxProvider, SafetyFilter
+from mcp_fuzzer.safety_system.filesystem.sandbox import FilesystemSandbox
+
+class CustomSandbox(SandboxProvider):
+    def initialize(self, root: str) -> None:
+        ...
+
+    def get_sandbox(self) -> FilesystemSandbox:
+        ...
+
+custom_filter = SafetyFilter(sandbox_provider=CustomSandbox())
+```
+
+## Minimal Policy Configuration Example
+
+```yaml
+safety_enabled: true
+enable_safety_system: true
+fs_root: "~/.mcp_fuzzer"
+no_network: true
+allow_hosts:
+  - "localhost"
+  - "127.0.0.1"
+```
+
 ## Best Practices
 
 - Always combine `--enable-safety-system` with a sandboxed `--fs-root` when

docs/configuration/configuration.md

@@ -52,6 +52,18 @@ timeout: 30.0
 tool_timeout: 10.0
 log_level: "INFO"
 
+# Transport retry policy (optional)
+# transport_retries: Total attempts for transport requests (1 disables retries)
+# transport_retry_delay: Base delay between retries (seconds)
+# transport_retry_backoff: Backoff multiplier
+# transport_retry_max_delay: Maximum delay between retries (seconds)
+# transport_retry_jitter: Jitter factor for retry delay
+transport_retries: 1
+transport_retry_delay: 0.5
+transport_retry_backoff: 2.0
+transport_retry_max_delay: 5.0
+transport_retry_jitter: 0.1
+
 # Safety and filesystem constraints
 safety_enabled: true
 enable_safety_system: false
@@ -198,8 +210,8 @@ export_csv: "reports/results.csv"
 export_html: "reports/results.html"
 ```
 
-Standardized output files are currently emitted as JSON; `output.format` is
-accepted for compatibility with legacy tooling.
+Standardized output files are currently emitted as JSON regardless of
+`output.format`; other values are reserved for future formats.
 
 ## Authentication Configuration
 
@@ -244,5 +256,3 @@ custom_transports:
 Use the transport by setting `protocol: mytransport` in the same config file.
 
 ## Notes
-
-- Standardized output files are currently emitted as JSON; `output.format` is accepted for compatibility.