feat(cli): add shep doctor command for self-diagnosis and auto-fix

apis/json-schema/AgentRunDetail.yaml

@@ -0,0 +1,28 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+$id: AgentRunDetail.yaml
+type: object
+properties:
+  agentType:
+    type: string
+    description: Type of agent (e.g. claude-code, gemini-cli)
+  agentName:
+    type: string
+    description: Name/identifier of the agent run
+  prompt:
+    type: string
+    description: Input prompt sent to the agent executor
+  result:
+    type: string
+    description: Final result output from the agent (if available)
+  error:
+    type: string
+    description: Error message if the run failed
+  timestamp:
+    type: string
+    description: ISO 8601 timestamp of the run
+required:
+  - agentType
+  - agentName
+  - prompt
+  - timestamp
+description: Detailed agent run information including prompt and result for diagnostic reporting

apis/json-schema/DoctorDiagnosticReport.yaml

@@ -0,0 +1,76 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+$id: DoctorDiagnosticReport.yaml
+type: object
+properties:
+  userDescription:
+    type: string
+    description: User-provided description of the problem
+  failedRunSummaries:
+    type: array
+    items:
+      $ref: FailedRunSummary.yaml
+    description: Summaries of recent failed agent runs
+  systemInfo:
+    $ref: SystemInfo.yaml
+    description: System environment information
+  cliVersion:
+    type: string
+    description: Current shep CLI version
+  featureId:
+    type: string
+    description: Feature ID when diagnosing a specific feature (optional)
+  featureName:
+    type: string
+    description: Feature name when diagnosing a specific feature (optional)
+  featureLifecycle:
+    type: string
+    description: Feature lifecycle phase (e.g. Implementation, Review)
+  featureBranch:
+    type: string
+    description: Feature git branch name
+  featureDescription:
+    type: string
+    description: Feature description
+  featureWorkflowConfig:
+    type: string
+    description: JSON-serialized feature workflow configuration (fast, push, openPr, approvalGates)
+  specYaml:
+    type: string
+    description: Raw spec.yaml content
+  researchYaml:
+    type: string
+    description: Raw research.yaml content
+  planYaml:
+    type: string
+    description: Raw plan.yaml content
+  tasksYaml:
+    type: string
+    description: Raw tasks.yaml content
+  featureStatusYaml:
+    type: string
+    description: Raw feature.yaml (status tracking) content
+  agentRunDetails:
+    type: array
+    items:
+      $ref: AgentRunDetail.yaml
+    description: Detailed agent run information including prompts and results
+  conversationMessages:
+    type: string
+    description: JSON-serialized conversation messages (Feature.messages[])
+  featurePlan:
+    type: string
+    description: JSON-serialized feature plan (Feature.plan)
+  workerLogs:
+    type: array
+    items:
+      $ref: WorkerLogEntry.yaml
+    description: Worker execution logs for agent runs associated with this feature
+  phaseTimings:
+    type: string
+    description: JSON-serialized phase timing records
+required:
+  - userDescription
+  - failedRunSummaries
+  - systemInfo
+  - cliVersion
+description: Structured diagnostic report collected by shep doctor for issue creation

apis/json-schema/FailedRunSummary.yaml

@@ -0,0 +1,22 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+$id: FailedRunSummary.yaml
+type: object
+properties:
+  agentType:
+    type: string
+    description: Type of agent that failed (e.g. claude-code, gemini-cli)
+  agentName:
+    type: string
+    description: Name/identifier of the agent run
+  error:
+    type: string
+    description: Error message from the failed run
+  timestamp:
+    type: string
+    description: ISO 8601 timestamp when the failure occurred
+required:
+  - agentType
+  - agentName
+  - error
+  - timestamp
+description: Summary of a failed agent run for diagnostic reporting

apis/json-schema/SystemInfo.yaml

@@ -0,0 +1,22 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+$id: SystemInfo.yaml
+type: object
+properties:
+  nodeVersion:
+    type: string
+    description: Node.js version (e.g. v20.11.0)
+  platform:
+    type: string
+    description: Operating system platform (e.g. darwin, linux, win32)
+  arch:
+    type: string
+    description: CPU architecture (e.g. x64, arm64)
+  ghVersion:
+    type: string
+    description: gh CLI version string
+required:
+  - nodeVersion
+  - platform
+  - arch
+  - ghVersion
+description: System environment information for diagnostic reporting

apis/json-schema/WorkerLogEntry.yaml

@@ -0,0 +1,27 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+$id: WorkerLogEntry.yaml
+type: object
+properties:
+  agentRunId:
+    type: string
+    description: Agent run ID this log belongs to
+  agentName:
+    type: string
+    description: Name of the agent that produced this log
+  content:
+    type: string
+    description: Full log file content (may be truncated)
+  truncated:
+    type: boolean
+    description: Whether the content was truncated due to size limits
+  originalLength:
+    type: integer
+    minimum: -2147483648
+    maximum: 2147483647
+    description: Original character count before truncation (only set when truncated)
+required:
+  - agentRunId
+  - agentName
+  - content
+  - truncated
+description: Worker log entry for a specific agent run

apis/json-schema/WorkflowConfig.yaml

@@ -55,6 +55,11 @@ properties:
   hideCiStatus:
     type: boolean
     description: "Hide CI status badges from UI (default: true)"
+  doctorMaxFixAttempts:
+    type: integer
+    minimum: -2147483648
+    maximum: 2147483647
+    description: "Maximum number of doctor fix attempts before giving up (default: 1)"
 required:
   - openPrOnImplementationComplete
   - approvalGateDefaults