docs: streamline agent guidance and standardize rustdoc links

crates/flow/README.md

@@ -4,7 +4,7 @@
 
 ## Main entry points
 
-- [`compile_flow_source`](src/definition.rs): Source evaluation and graph validation.
-- [`FlowSelector`](src/selector.rs) / [`ResolvedFlowSource`](src/selector.rs): Explicit source identity and immutable snapshots.
-- [`FlowRuntimeState`](src/coordinator.rs): Instances, transition attempts, and ordered events.
-- [`builtin_flow_source`](src/builtin.rs): Read-only catalog of embedded sources.
+- [`compile_flow_source`]: Source evaluation and graph validation.
+- [`FlowSelector`] / [`ResolvedFlowSource`]: Explicit source identity and immutable snapshots.
+- [`FlowRuntimeState`]: Instances, transition attempts, and ordered events.
+- [`builtin_flow_source`]: Read-only catalog of embedded sources.

crates/mcp/README.md

@@ -4,4 +4,4 @@
 
 ## Main entry points
 
-- [`stdio`](src/stdio.rs): Server launch configuration resolution, bounded responses, diagnostics, and shutdown.
+- [`stdio`]: Server launch configuration resolution, bounded responses, diagnostics, and shutdown.

crates/tools/README.md

@@ -4,7 +4,7 @@
 
 ## Main entry points
 
-- [`core_builtin_tools`](src/lib.rs) / [`routed_builtin_tools`](src/lib.rs): registration by provider capability and connection resolution.
-- [`checkout`](src/checkout.rs): shared handling for route-bound native operations and regular Tools.
-- [`tracker`](src/tracker.rs): read hashes and change tracking per connection generation.
-- [`view_image`](src/view_image.rs): bounded byte retrieval and image detection.
+- [`core_builtin_tools`] / [`routed_builtin_tools`]: registration by provider capability and connection resolution.
+- [`checkout`]: shared handling for route-bound native operations and regular Tools.
+- [`tracker`]: read hashes and change tracking per connection generation.
+- [`view_image`]: bounded byte retrieval and image detection.

crates/tui/README.md

@@ -4,7 +4,5 @@
 
 ## Implementation entry points
 
-- [`launch`] / [`LaunchMode`] — typed launch requests and terminal restoration.
-- `src/app.rs`: display state built from protocol snapshots and events.
-- `src/input.rs` / `src/composer_history.rs`: typed input and local editing history.
-- `src/console/`: connection, input-event, and attachment-staging management.
+- [`launch`] — Console and Dashboard execution with terminal restoration.
+- [`LaunchOptions`] / [`LaunchMode`] — typed connection and launch requests.

crates/worker-runtime/README.md

@@ -4,7 +4,7 @@ Manages Worker creation, stopping, and Restore, execution connections within the
 
 ## Reference index
 
-- [`Runtime`](crate::Runtime): lifecycle operation acceptance, Workspace boundaries, and execution connections.
+- [`Runtime`]: lifecycle operation acceptance, Workspace boundaries, and execution connections.
 - [`execution`] — execution backends and operation-specific results.
 - [`working_directory`] — repository materialization, session resources, and safe deletion.
 - [`workspace_issuer`] — Workspace signature verification and replay prevention.

crates/worker/README.md

@@ -4,8 +4,8 @@
 
 ## Main entry points
 
-- [`Worker`](src/worker.rs): Input admission, execution, and Session restoration.
-- [`controller`](src/controller.rs): Worker control and protocol intake.
-- [`feature`](src/feature.rs): Feature declarations, registration, and structured invocation.
-- [`wip`](src/wip.rs): WIP namespaces, native/compatibility projections, and the Client/Host boundary.
-- [`spawn`](src/spawn/mod.rs): Delegation and control of parent-owned Internal SubWorkers.
+- [`Worker`]: Input admission, execution, and Session restoration.
+- [`controller`]: Worker control and protocol intake.
+- [`feature`]: Feature declarations, registration, and structured invocation.
+- [`wip`]: WIP namespaces, native/compatibility projections, and the Client/Host boundary.
+- [`spawn`]: Delegation and control of parent-owned Internal SubWorkers.

crates/yoi/README.md

@@ -4,7 +4,6 @@
 
 ## Implementation entry points
 
-- `src/main.rs`: product command parsing and dispatch to launch targets.
-- `src/cli_connection.rs`: per-command connection requirements and target resolution.
-- `src/workspace_bootstrap.rs`: Workspace creation and Backend routing records.
+Command dispatch, connection selection, and Workspace bootstrap are binary-internal. The library exposes:
+
 - [`workdir_share`] — sharing existing Workdirs.