docs: add comprehensive L3 specs across all crates with architecture design, traceability, and L2 refinements

Author: wangtsiao

specs/L2/agent/L2-DES-AGENT-001-execution-engine.md

@@ -289,7 +289,8 @@ The final user-facing response should summarize the outcome, changed files where
 | related-to | L2-DES-MODEL-001 | 1 | specs/L2/model/L2-DES-MODEL-001-model-provider-binding.md | Model resolution provides runtime invocation profiles. |
 | related-to | L2-DES-TOOL-001 | 1 | specs/L2/tool/L2-DES-TOOL-001-built-in-tool-system.md | Defines tool registry, lifecycle, and plan tool behavior used by dispatch. |
 | related-to | L2-DES-GOAL-001 | 1 | specs/L2/goal/L2-DES-GOAL-001-ralph-loop-goals.md | Defines autonomous goal continuation and model-facing goal update behavior layered on the engine. |
-| specified-by | TBD | TBD | specs/L3/agent/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-CORE-002 | 1 | specs/L3/core/L3-BEH-CORE-002-turn-execution-engine.md | L3 defines the core turn execution state machine and decision boundaries. |
+| specified-by | L3-BEH-SERVER-001 | 1 | specs/L3/server/L3-BEH-SERVER-001-server-runtime-transport.md | L3 defines server orchestration around core turn execution. |
 
 ## Revision Notes
 

specs/L2/agent/L2-DES-AGENT-002-interrupt-resume-control.md

@@ -242,7 +242,8 @@ Clients should:
 | related-to | L2-DES-AGENT-001 | 1 | specs/L2/agent/L2-DES-AGENT-001-execution-engine.md | Defines the execution runtime being interrupted and resumed. |
 | related-to | L2-DES-APP-003 | 1 | specs/L2/app/L2-DES-APP-003-client-server-protocol.md | Protocol methods and events expose interrupt and resume control to clients. |
 | related-to | L2-DES-CONV-001 | 1 | specs/L2/conv/L2-DES-CONV-001-session-jsonl-data-model.md | Durable records preserve interrupted and resumed state. |
-| specified-by | TBD | TBD | specs/L3/agent/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-SERVER-001 | 1 | specs/L3/server/L3-BEH-SERVER-001-server-runtime-transport.md | L3 defines server cancellation token wiring and active work ownership. |
+| specified-by | L3-BEH-SERVER-002 | 2 | specs/L3/server/L3-BEH-SERVER-002-interrupt-resume.md | L3 defines interruption targets, resume turns, active work inspection, and crash recovery. |
 
 ## Revision Notes
 

specs/L2/agent/L2-DES-AGENT-003-subagent-architecture.md

@@ -611,6 +611,7 @@ These are injected as developer messages at child session start and are stripped
 | related-to | L2-DES-SAFETY-002 | 1 | specs/L2/safety/L2-DES-SAFETY-002-approval-mechanism.md | Subagents route through the same approval flow. |
 | related-to | L2-DES-CONV-001 | 1 | specs/L2/conv/L2-DES-CONV-001-session-jsonl-data-model.md | Session data model includes fork references and subagent metadata. |
 | related-to | L2-DES-APP-003 | 1 | specs/L2/app/L2-DES-APP-003-client-server-protocol.md | Protocol events expose subagent spawn, status, and completion. |
+| specified-by | L3-BEH-SERVER-003 | 2 | specs/L3/server/L3-BEH-SERVER-003-subagent-coordination.md | L3 defines spawn lifecycle, agent tree registry, mailbox, completion watching, and session resumption. |
 
 ## Revision Notes
 

specs/L2/app/L2-DES-APP-001-memory-efficient-rust-data-models.md

@@ -74,7 +74,7 @@ Memory optimizations must be measurable when they are introduced for performance
 | Relationship | Target ID | Target Revision | Target Path | Rationale |
 |---|---|---:|---|---|
 | refines | L1-REQ-APP-005 | 1 | specs/L1/L1-REQ-APP-005-lightweight.md | Provides technical design guidance for avoiding unnecessary memory growth. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-DES-ARCH-001 | 1 | specs/L3/L3-DES-ARCH-001-crate-architecture.md | L3 defines crate ownership and efficient data boundary placement. |
 
 ## References
 

specs/L2/app/L2-DES-APP-002-configuration-precedence.md

@@ -157,7 +157,7 @@ Rules:
 | related-to | L1-REQ-TUI-006 | 1 | specs/L1/L1-REQ-TUI-006-command-discovery-control.md | Slash commands can trigger session selection or configuration writes. |
 | related-to | L1-REQ-APP-012 | 1 | specs/L1/L1-REQ-APP-012-privacy-data-ownership.md | Credential persistence and projection behavior must follow privacy expectations. |
 | related-to | L2-DES-APP-005 | 1 | specs/L2/app/L2-DES-APP-005-config-toml-schema.md | Defines the concrete `config.toml` and `auth.json` schemas resolved by this precedence design. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-APP-001 | 1 | specs/L3/app/L3-BEH-APP-001-configuration-resolution.md | Defines configuration path resolution, validation, effective merge behavior, inspection projections, and safe persistence mechanics. |
 
 ## Revision Notes
 

specs/L2/app/L2-DES-APP-003-client-server-protocol.md

@@ -473,10 +473,14 @@ If a client disconnects, the server continues owning active work subject to user
 | related-to | L2-DES-TOOL-002 | 1 | specs/L2/tool/L2-DES-TOOL-002-parallel-tool-orchestration.md | Parallel tool groups require parent and child event identifiers for client rendering and replay. |
 | related-to | L2-DES-GOAL-001 | 1 | specs/L2/goal/L2-DES-GOAL-001-ralph-loop-goals.md | The protocol exposes user-owned goal controls and canonical goal notifications. |
 | related-to | L2-DES-APP-006 | 1 | specs/L2/app/L2-DES-APP-006-fuzzy-search-architecture.md | The protocol exposes fuzzy-search sessions and live result snapshots. |
+| specified-by | L3-BEH-CORE-011 | 1 | specs/L3/core/L3-BEH-CORE-011-session-forking-retention.md | L3 defines concrete behavior behind `session.fork`, `session.delete` fork-retention preflight, inherited segment actions, and parent-unavailable fork projection. |
+| specified-by | L3-BEH-CORE-012 | 1 | specs/L3/core/L3-BEH-CORE-012-message-edit-workspace-restore.md | L3 defines concrete behavior behind `message.editPrevious`, restore policy, workspace restore events, superseded turns, and replacement turn sequencing. |
 | related-to | L2-DES-CLIENT-002 | 1 | specs/L2/client/L2-DES-CLIENT-002-prefixed-input-actions.md | The protocol supports server-owned search providers used by prefixed input. |
 | related-to | L2-DES-CONV-001 | 1 | specs/L2/conv/L2-DES-CONV-001-session-jsonl-data-model.md | Durable session events are distinct from live server-client protocol events. |
 | related-to | L2-DES-APP-005 | 1 | specs/L2/app/L2-DES-APP-005-config-toml-schema.md | `config.inspect` and `config.update` operate on safe projections and updates derived from the `config.toml` and `auth.json` schemas. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-PROTOCOL-001 | 2 | specs/L3/protocol/L3-BEH-PROTOCOL-001-jsonrpc-protocol.md | L3 defines JSON-RPC envelope validation, session subscription, sequencing, broadcasting, turn submission, idempotency, approval races, fork/delete, and message edit requests. |
+| specified-by | L3-BEH-SERVER-001 | 1 | specs/L3/server/L3-BEH-SERVER-001-server-runtime-transport.md | L3 defines server runtime transport ownership and event broadcast behavior. |
+| specified-by | L3-BEH-CLIENT-001 | 1 | specs/L3/client/L3-BEH-CLIENT-001-connection-subscription.md | L3 defines client connection, subscription, reconnection, and catch-up behavior. |
 
 ## References
 

specs/L2/app/L2-DES-APP-004-observability-architecture.md

@@ -265,7 +265,7 @@ Telemetry must not include model prompts, model responses, tool outputs, credent
 | related-to | L2-DES-AGENT-001 | 1 | specs/L2/agent/L2-DES-AGENT-001-execution-engine.md | Execution phases provide the event capture points for observability. |
 | related-to | L2-DES-LLM-003 | 1 | specs/L2/llm/L2-DES-LLM-003-model-usage-observability.md | Defines the model-specific usage and streaming trace data used by this architecture. |
 | related-to | L2-DES-TOOL-001 | 1 | specs/L2/tool/L2-DES-TOOL-001-built-in-tool-system.md | Tool lifecycle events and result summaries feed user-facing diagnostics. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-APP-002 | 1 | specs/L3/app/L3-BEH-APP-002-observability-runtime.md | Defines structured log records, active diagnostic projection, trace records, redaction, retention, and telemetry runtime behavior. |
 
 ## Revision Notes
 

specs/L2/app/L2-DES-APP-005-config-toml-schema.md

@@ -574,7 +574,7 @@ When a setup flow writes both `config.toml` and `auth.json`, the program should
 | related-to | L2-DES-MODEL-001 | 1 | specs/L2/model/L2-DES-MODEL-001-model-provider-binding.md | Provides concrete persistence fields for providers and model bindings. |
 | related-to | L2-DES-MCP-001 | 1 | specs/L2/mcp/L2-DES-MCP-001-mcp-integration-architecture.md | Provides concrete persistence fields for MCP servers. |
 | related-to | L2-DES-SKILLS-001 | 1 | specs/L2/skills/L2-DES-SKILLS-001-agent-skills-architecture.md | Provides concrete persistence fields for skill roots and enablement. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-APP-001 | 1 | specs/L3/app/L3-BEH-APP-001-configuration-resolution.md | Defines schema validation, merge behavior, safe inspection, and atomic per-file write behavior for `config.toml` and `auth.json`. |
 
 ## Revision Notes
 

specs/L2/app/L2-DES-APP-006-fuzzy-search-architecture.md

@@ -224,7 +224,7 @@ Rules:
 | related-to | L1-REQ-CLIENT-004 | 1 | specs/L1/L1-REQ-CLIENT-004-prefixed-input-actions.md | The `@` prefix uses fuzzy-search providers for live selection. |
 | related-to | L1-REQ-CLIENT-001 | 1 | specs/L1/L1-REQ-CLIENT-001-localization-readiness.md | Search queries and paths must preserve Unicode text. |
 | related-to | L2-DES-CLIENT-001 | 1 | specs/L2/client/L2-DES-CLIENT-001-localization-readiness.md | Defines Unicode, IME, and display constraints for client search input. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-CORE-010 | 1 | specs/L3/core/L3-BEH-CORE-010-fuzzy-search.md | L3 defines incremental file search workers, matcher behavior, session lifecycle, and provider model. |
 
 ## Revision Notes
 

specs/L2/app/L2-DES-APP-007-cli-onboarding-entry.md

@@ -90,7 +90,7 @@ If the user is already inside an active TUI session and needs to repair or add m
 | related-to | L2-DES-TUI-001 | 1 | specs/L2/tui/L2-DES-TUI-001-onboarding-ui-flow.md | The CLI entry starts the TUI onboarding flow defined there. |
 | related-to | L2-DES-APP-002 | 1 | specs/L2/app/L2-DES-APP-002-configuration-precedence.md | Defines persistence target and source precedence for onboarding output. |
 | related-to | L2-DES-APP-005 | 1 | specs/L2/app/L2-DES-APP-005-config-toml-schema.md | Defines persisted config and credential schema written by onboarding. |
-| specified-by | TBD | TBD | specs/L3/app/TBD.md | L3 behavior has not been authored yet. |
+| specified-by | L3-BEH-CLI-001 | 2 | specs/L3/cli/L3-BEH-CLI-001-entry-onboarding.md | L3 defines CLI argument parsing, onboarding entry, server lifecycle, signal handling, and exit behavior. |
 
 ## Revision Notes