chore(runner): removed all direct reads or writes to DocImpl, now everything goes via transactions (#1427)

* refactor(runner): remove remaining direct uses of `doc`

- Refactored core runner modules to eliminate direct references to the `doc` object.
- Updated builder, builtins, cell, data-updating, doc-map, link-utils, query-result-proxy, recipe-binding, runner, runtime, scheduler, sigil-types, storage, storage/transaction-shim, and uri-utils to use new abstractions or access patterns.
- Adjusted related tests to align with the new approach and ensure coverage.

* refactor: consolidate sigil link creation and improve schema handling

- Move createSigilLink function from cell.ts to link-utils.ts as createSigilLinkFromParsedLink
- Add support for base cell/link parameter to enable relative references
- Add sanitizeSchemaForLinks function to remove asCell/asStream flags from schemas
- Update all callers to use new function signature with options object
- Add comprehensive tests for schema sanitization

Author: seefeldb

packages/runner/src/builder/factory.ts

@@ -1,7 +1,6 @@
 /**
  * Factory function to create builder functions with runtime dependency injection
  */
-import { getCellLinkOrThrow, type Runtime } from "../index.ts";
 import type {
   BuilderFunctionsAndConstants,
   Cell,
@@ -34,14 +33,15 @@ import {
 } from "./built-in.ts";
 import { getRecipeEnvironment } from "./env.ts";
 import type { RuntimeProgram } from "../harness/types.ts";
+import type { IRuntime } from "../runtime.ts";
 
 /**
  * Creates a set of builder functions with the given runtime
  * @param runtime - The runtime instance to use for cell creation
  * @returns An object containing all builder functions
  */
 export const createBuilder = (
-  runtime: Runtime,
+  runtime: IRuntime,
 ): {
   commontools: BuilderFunctionsAndConstants;
   exportsCallback: (exports: Map<any, RuntimeProgram>) => void;

packages/runner/src/builder/json-utils.ts

@@ -20,7 +20,7 @@ import {
 import { getTopFrame } from "./recipe.ts";
 import { deepEqual } from "../path-utils.ts";
 import { IRuntime } from "../runtime.ts";
-import { parseLink } from "../link-utils.ts";
+import { parseLink, sanitizeSchemaForLinks } from "../link-utils.ts";
 
 export function toJSONWithLegacyAliases(
   value: Opaque<any>,
@@ -55,8 +55,12 @@ export function toJSONWithLegacyAliases(
         $alias: {
           ...(isShadowRef(value) ? { cell: value } : {}),
           path: pathToCell as (string | number)[],
-          ...(exported?.schema ? { schema: exported.schema } : {}),
-          ...(exported?.rootSchema ? { rootSchema: exported.rootSchema } : {}),
+          ...(exported?.schema
+            ? { schema: sanitizeSchemaForLinks(exported.schema) }
+            : {}),
+          ...(exported?.rootSchema
+            ? { rootSchema: sanitizeSchemaForLinks(exported.rootSchema) }
+            : {}),
         },
       } satisfies LegacyAlias;
     } else throw new Error(`Cell not found in paths`);

packages/runner/src/builtins/stream-data.ts

@@ -65,10 +65,6 @@ export function streamData(
         tx,
       );
 
-      pending.getDoc().ephemeral = true;
-      result.getDoc().ephemeral = true;
-      error.getDoc().ephemeral = true;
-
       pending.setSourceCell(parentCell);
       result.setSourceCell(parentCell);
       error.setSourceCell(parentCell);