Add errors to TomlFile and Project for TOML parse failure tracking

[ryancbahan]

What

Unify TOML error types, add errors to TomlFile and Project, and surface TOML parse failures in app config validate --json.

How

Unified error type: TomlFileNotFoundError and TomlParseError replaced with single TomlFileError class. Parse errors produce clean one-line messages ("Invalid boolean, expected true or false at row 6, col 13") instead of multi-line ASCII art.

TomlFile.errors: New field on TomlFile. read() still throws. Callers that catch create a TomlFile with the path and error populated — the file exists in the model even when malformed.

Project.errors: Aggregated from all discovery passes. Malformed files are included in appConfigFiles/extensionConfigFiles/webConfigFiles (with errors and empty content) instead of silently dropped.

Validate command: Checks project.errors before attempting to link. Reports TOML parse errors as {valid: false, issues: [{file, message}]} in JSON mode.

Depends on #7128, #7126.

Tophatting

valid config
Screen Recording 2026-03-30 at 4.20.35 PM.mov (uploaded via Graphite)

invalid config -- shopify domain
Screen Recording 2026-03-30 at 4.21.52 PM.mov (uploaded via Graphite)

invalid config -- invalid toml syntax
Screen Recording 2026-03-30 at 4.22.47 PM.mov (uploaded via Graphite)

[github-actions]

We detected some changes at packages/*/src and there are no updates in the .changeset.
If the changes are user-facing, run pnpm changeset add to track your changes and include them in the next release CHANGELOG.

Caution

DO NOT create changesets for features which you do not wish to be included in the public changelog of the next CLI release.

[ryancbahan]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• Add errors to TomlFile and Project for TOML parse failure tracking #7130 👈 (View in Graphite)
• Add structured {valid, issues} JSON contract for app config validate #7128
• Refactor app validation errors: result-based parsing, structured error data #7126
• main

This stack of pull requests is managed by Graphite. Learn more about stacking.

[github-actions]

Differences in type declarations

We detected differences in the type declarations generated by Typescript for this branch compared to the baseline ('main' branch). Please, review them to ensure they are backward-compatible. Here are some important things to keep in mind:

• Some seemingly private modules might be re-exported through public modules.
• If the branch is behind main you might see odd diffs, rebase main into this branch.

New type declarations

We found no new type declarations in this PR

Existing type declarations

packages/cli-kit/dist/public/node/toml/toml-file.d.ts

 import { JsonMapType } from './codec.js';
 /**
- * Thrown when a TOML file does not exist at the expected path.
+ * An error on a TOML file — missing or malformed.
+ * Extends Error so it can be thrown. Carries path and a clean message suitable for JSON output.
  */
-export declare class TomlFileNotFoundError extends Error {
+export declare class TomlFileError extends Error {
     readonly path: string;
-    constructor(path: string);
+    constructor(path: string, message: string);
 }
 /**
- * Thrown when a TOML file cannot be parsed. Includes the file path for context.
- */
-export declare class TomlParseError extends Error {
-    readonly path: string;
-    constructor(path: string, cause: Error);
-}
-/**
  * General-purpose TOML file abstraction.
  *
  * Provides a unified interface for reading, patching, removing keys from, and replacing
  * the content of TOML files on disk.
  *
  * - `read` populates content from disk
  * - `patch` does surgical WASM-based edits (preserves comments and formatting)
  * - `remove` deletes a key by dotted path (preserves comments and formatting)
  * - `replace` does a full re-serialization (comments and formatting are NOT preserved).
  * - `transformRaw` applies a function to the raw TOML string on disk.
  */
 export declare class TomlFile {
     /**
-     * Read and parse a TOML file from disk. Throws if the file doesn't exist or contains invalid TOML.
-     * Parse errors are wrapped in {@link TomlParseError} with the file path for context.
+     * Read and parse a TOML file from disk. Throws {@link TomlFileError} if the file
+     * doesn't exist or contains invalid TOML.
      *
      * @param path - Absolute path to the TOML file.
      * @returns A TomlFile instance with parsed content.
      */
     static read(path: string): Promise<TomlFile>;
     readonly path: string;
     content: JsonMapType;
+    readonly errors: TomlFileError[];
     constructor(path: string, content: JsonMapType);
     /**
      * Surgically patch values in the TOML file, preserving comments and formatting.
      *
      * Accepts a nested object whose leaf values are set in the TOML. Intermediate tables are
      * created automatically. Setting a leaf to `undefined` removes it (use `remove()` for a
      * clearer API when deleting keys).
      *
      * @example
      * ```ts
      * await file.patch({build: {dev_store_url: 'my-store.myshopify.com'}})
      * await file.patch({application_url: 'https://example.com', auth: {redirect_urls: ['...']}})
      * ```
      */
     patch(changes: {
         [key: string]: unknown;
     }): Promise<void>;
     /**
      * Remove a key from the TOML file by dotted path, preserving comments and formatting.
      *
      * @param keyPath - Dotted key path to remove (e.g. 'build.include_config_on_deploy').
      * @example
      * ```ts
      * await file.remove('build.include_config_on_deploy')
      * ```
      */
     remove(keyPath: string): Promise<void>;
     /**
      * Replace the entire file content. The file is fully re-serialized — comments and formatting
      * are NOT preserved.
      *
      * @param content - The new content to write.
      * @example
      * ```ts
      * await file.replace({client_id: 'abc', name: 'My App'})
      * ```
      */
     replace(content: JsonMapType): Promise<void>;
     /**
      * Transform the raw TOML string on disk. Reads the file, applies the transform function
      * to the raw text, writes back, and re-parses to keep `content` in sync.
      *
      * Use this for text-level operations that can't be expressed as structured edits —
      * e.g. Injecting comments or positional insertion of keys in arrays-of-tables.
      * Subsequent `patch()` calls will preserve any comments added this way.
      *
      * @param transform - A function that receives the raw TOML string and returns the modified string.
      * @example
      * ```ts
      * await file.transformRaw((raw) => `# Header comment\n${raw}`)
      * ```
      */
     transformRaw(transform: (raw: string) => string): Promise<void>;
     private decode;
 }