diff --git a/README.md b/README.md
index 47d7289..10a4bb4 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ matrixai-lint --fix
 | `--user-config`          | Uses detected `eslint.config.[js,mjs,cjs,ts]` from the project root if found |
 | `--eslint-config <path>` | Explicitly use a custom ESLint config file                                   |
 | `--eslint <targets>`     | ESLint targets (files, roots, or globs); implies ESLint domain selection     |
-| `--shell <targets>`      | Shell targets (files, roots, or globs) used to derive shell search roots     |
+| `--shell <targets>`      | Shell targets (files, roots, or globs); implies shell domain selection       |
 | `--domain <id...>`       | Run only selected domains (`eslint`, `shell`, `markdown`)                    |
 | `--skip-domain <id...>`  | Skip selected domains (`eslint`, `shell`, `markdown`)                        |
 | `--list-domains`         | Print available domains and short descriptions, then exit 0                  |
@@ -66,6 +66,32 @@ Domain selection behavior:
   - File paths and glob patterns are reduced to search roots, then `*.sh` files
     are discovered under those roots.
 
+#### Targeted workflows
+
+- Only ESLint on a subset of files:
+
+  ```sh
+  matrixai-lint --eslint "src/**/*.{ts,tsx}" --domain eslint
+  ```
+
+- Only shell scripts under specific roots:
+
+  ```sh
+  matrixai-lint --shell scripts packages/*/scripts
+  ```
+
+- Markdown only:
+
+  ```sh
+  matrixai-lint --domain markdown
+  ```
+
+- Mixed scoped run (ESLint + shell only):
+
+  ```sh
+  matrixai-lint --eslint "src/**/*.{ts,tsx}" --shell scripts
+  ```
+
 #### Examples
 
 ```sh
@@ -98,7 +124,7 @@ export default config;
 
 ```js
 // eslint.config.js
-import matrixai from '@matrixai/lint/configs/js.js';
+import matrixai from '@matrixai/lint/configs/eslint.js';
 
 export default matrixai;
 ```
@@ -146,8 +172,8 @@ Supported imports:
 
 - `@matrixai/lint`: named export `config`; types `MatrixAILintCfg`,
   `RawMatrixCfg`, `CLIOptions`.
-- `@matrixai/lint/configs/js.js`: default export of the ESLint Flat Config array
-  (same shape as `config`).
+- `@matrixai/lint/configs/eslint.js`: default export of the ESLint Flat Config
+  array (same shape as `config`).
 - `@matrixai/lint/configs/prettier.config.js`: reusable Prettier options object.
 
 The exported `config` is intended as a composable base preset for downstream
diff --git a/package-lock.json b/package-lock.json
index a97af0c..4cf2ac2 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "@matrixai/lint",
-  "version": "0.2.12",
+  "version": "0.3.0",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@matrixai/lint",
-      "version": "0.2.12",
+      "version": "0.3.0",
       "license": "Apache-2.0",
       "dependencies": {
         "@eslint/compat": "^1.2.5",
diff --git a/package.json b/package.json
index 589bd5e..492d85d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@matrixai/lint",
-  "version": "0.2.12",
+  "version": "0.3.0",
   "author": "Roger Qiu",
   "description": "Org wide custom eslint rules",
   "license": "Apache-2.0",
@@ -38,7 +38,7 @@
     "tsx": "tsx",
     "lint": "npm run prepare && node ./dist/bin/lint.js --domain eslint shell markdown --eslint \"{src,scripts,tests}/**/*.{js,mjs,ts,mts,jsx,tsx}\" --shell src scripts tests",
     "lintfix": "npm run prepare && node ./dist/bin/lint.js --fix --domain eslint shell markdown --eslint \"{src,scripts,tests}/**/*.{js,mjs,ts,mts,jsx,tsx}\" --shell src scripts tests",
-    "lint-shell": "find ./src ./tests ./scripts -type f -regextype posix-extended -regex '.*\\.(sh)' -exec shellcheck {} +",
+    "lint-shell": "npm run prepare && node ./dist/bin/lint.js --domain shell --shell src scripts tests",
     "docs": "shx rm -rf ./docs && typedoc --gitRevision master --tsconfig ./tsconfig.build.json --out ./docs src",
     "test": "node ./scripts/test.mjs"
   },
diff --git a/plans/refactor/PLAN.md b/plans/refactor/PLAN.md
index 82f7aed..633f222 100644
--- a/plans/refactor/PLAN.md
+++ b/plans/refactor/PLAN.md
@@ -5,15 +5,15 @@
 Refactor `matrixai-lint` into a domain-oriented lint engine that:
 
 - Performs smart auto-discovery (project relevance) independently from tool availability.
-- Distinguishes built-in npm-based capabilities (for example ESLint/Prettier) from optional external tools (for example ShellCheck, nixfmt).
+- Distinguishes built-in npm-based capabilities (for example ESLint/Prettier) from optional external tools (for example ShellCheck).
 - Supports explicit domain selection (include/exclude/only) with consistent target semantics.
-- Provides clean extension points for adding new domains.
+- Provides clear built-in domain boundaries and downstream ESLint extensibility via config composition.
 
 ## Non-goals
 
 - No behavior-changing implementation in this epic document (this is design/spec only).
 - No changes to the shipped ESLint ruleset content (rule tuning is out of scope).
-- No attempt to fully replace ESLint/Prettier/ShellCheck/nixfmt; this project orchestrates them.
+- No attempt to fully replace ESLint/Prettier/ShellCheck; this project orchestrates them.
 
 ## Constraints / invariants
 
@@ -82,7 +82,6 @@ Examples of relevance signals:
 - ESLint (JS/TS): any `*.{js,mjs,cjs,jsx,ts,tsx,mts,cts,json}` in the target set.
 - Markdown/Prettier: any `*.{md,mdx}` in the target set (plus `README.md` by convention).
 - ShellCheck: any `*.sh` in the target set.
-- Nixfmt: any `*.nix` in the target set.
 
 Relevance must be computed against the *effective target set* (CLI paths/globs + config defaults), not against the whole filesystem blindly.
 
@@ -93,7 +92,7 @@ Relevance must be computed against the *effective target set* (CLI paths/globs +
 Availability is domain-specific:
 
 - **Built-in npm-based** domains (ESLint, Prettier) are expected to be available whenever `@matrixai/lint` is installed.
-- **External optional** domains (ShellCheck, nixfmt) may not exist in downstream environments.
+- **External optional** domains (ShellCheck) may not exist in downstream environments.
 
 ### Decision matrix
 
@@ -109,17 +108,17 @@ This model explicitly distinguishes "capability exists" from "domain matters".
 
 ---
 
-## Proposed domain/plugin architecture
+## Proposed domain architecture
 
 ### High-level components
 
 - **Lint engine**: parses CLI/config, computes target set, selects domains, orchestrates execution, aggregates results.
-- **Domain plugins**: encapsulate discovery, tool checks, execution, and reporting for one domain.
+- **Domain modules**: encapsulate discovery, tool checks, execution, and reporting for one domain.
 - **Capability registry**: standardizes dependency checks (npm module resolution vs external binary lookup).
 
-### Domain plugin interface (conceptual)
+### Domain module interface (conceptual)
 
-Each domain plugin should define:
+Each domain module should define:
 
 - `id`: stable string identifier (for example `eslint`, `shellcheck`).
 - `discover(ctx)`: returns relevance result and default target patterns for this domain.
@@ -144,9 +143,6 @@ The engine is responsible for:
 3. **shellcheck**
    - External optional tool.
    - Lints `*.sh`.
-4. **nixfmt**
-   - External optional tool.
-   - Formats/checks `*.nix`.
 
 ### Mermaid: selection and execution pipeline
 
@@ -186,7 +182,7 @@ Dependencies are classified at evaluation time:
 ### Policy rules
 
 - **Auto-discovery must never fail the command** due solely to missing optional external tools.
-- **Explicit domain selection must be strict**: if a user asks for `shellcheck` or `nixfmt`, and the tool is missing, exit non-zero.
+- **Explicit domain selection must be strict**: if a user asks for `shellcheck`, and the tool is missing, exit non-zero.
 - Provide an actionable error message (what is missing, how the tool was detected, how to install).
 
 ---
@@ -240,7 +236,7 @@ Nixfmt-specific:
 
 ---
 
-## Config schema proposal (v2) + examples + extension points
+## Config schema proposal (v2) + examples
 
 ### File discovery
 
@@ -279,26 +275,16 @@ Continue to support `matrixai-lint-config.json`, but evolve it to a versioned sc
       "tool": {
         "command": "shellcheck"
       }
-    },
-    "nixfmt": {
-      "enabled": "auto",
-      "targets": ["**/*.nix"],
-      "tool": {
-        "command": "nixfmt"
-      }
     }
-  },
-  "plugins": [
-    { "module": "./lint-domains/custom-domain.mjs" }
-  ]
+  }
 }
 ```
 
 Notes:
 
 - `enabled` supports: `auto` | `on` | `off`.
-- `plugins` is the extension point: additional domain modules can be loaded to register domains.
 - Domain `tool.command` allows a configurable executable name/path for external tools.
+- Extensibility for downstream ESLint behavior is via ESLint Flat Config composition from the shipped preset (`@matrixai/lint/configs/eslint.js`) and CLI config selection flags such as `--eslint-config` and `--user-config`.
 
 ### Backward compatibility (v1)
 
@@ -334,7 +320,6 @@ Define a stable default domain order for readability and compatibility, while al
 1. `eslint`
 2. `shellcheck`
 3. `markdown-prettier`
-4. `nixfmt`
 
 ### Exit codes
 
@@ -366,15 +351,15 @@ If downstream requires a single non-zero code, document that any non-zero is fai
 
 Assume the project contains `src/**/*.ts`, `docs/**/*.md`, `scripts/foo.sh`, and `nix/shell.nix`.
 
-| Invocation | Domain selection intent | Expected executed domains | If `shellcheck` missing | If `nixfmt` missing |
-| --- | --- | --- | --- | --- |
-| `matrixai-lint` | auto | eslint, markdown-prettier, shellcheck, nixfmt (if relevant) | shellcheck skipped with warning | nixfmt skipped with warning |
-| `matrixai-lint --fix` | auto + fix | eslint (fix), markdown-prettier (write), shellcheck (check), nixfmt (format) | shellcheck skipped with warning | nixfmt skipped with warning |
-| `matrixai-lint --domain eslint` | explicit | eslint only | n/a | n/a |
-| `matrixai-lint --domain shellcheck` | explicit | shellcheck only | fail (missing tool) | n/a |
-| `matrixai-lint --skip-domain shellcheck` | auto minus one | eslint, markdown-prettier, nixfmt | n/a | nixfmt skipped with warning |
-| `matrixai-lint docs` | auto scoped | markdown-prettier (and maybe eslint if JS files under docs) | likely not relevant | likely not relevant |
-| `matrixai-lint --eslint "src/**/*.ts"` | implicit eslint targeting | eslint (explicit targets) + other auto domains unless skipped | shellcheck still auto (unless targets exclude it) | nixfmt still auto (unless targets exclude it) |
+| Invocation | Domain selection intent | Expected executed domains | If `shellcheck` missing |
+| --- | --- | --- | --- |
+| `matrixai-lint` | auto | eslint, markdown-prettier, shellcheck (if relevant) | shellcheck skipped with warning |
+| `matrixai-lint --fix` | auto + fix | eslint (fix), markdown-prettier (write), shellcheck (check) | shellcheck skipped with warning |
+| `matrixai-lint --domain eslint` | explicit | eslint only | n/a |
+| `matrixai-lint --domain shellcheck` | explicit | shellcheck only | fail (missing tool) |
+| `matrixai-lint --skip-domain shellcheck` | auto minus one | eslint, markdown-prettier | n/a |
+| `matrixai-lint docs` | auto scoped | markdown-prettier (and maybe eslint if JS files under docs) | likely not relevant |
+| `matrixai-lint --eslint "src/**/*.ts"` | implicit eslint targeting | eslint (explicit targets) + other auto domains unless skipped | shellcheck still auto (unless targets exclude it) |
 | `matrixai-lint --eslnt` | invalid option typo | none | n/a | n/a |
 
 Notes:
@@ -397,17 +382,17 @@ Notes:
 ### Suggested rollout phases
 
 1. **Phase 1: Internal refactor (no CLI changes)**
-   - Introduce the domain abstraction internally and re-implement current behavior using plugins.
+   - Introduce the domain abstraction internally and re-implement current behavior using built-in domains.
    - Preserve existing fixed sequencing as the default order.
    - Remove correctness hazards while preserving user-facing defaults:
      - enforce single final aggregation path (no early success return masking failures)
      - normalize thrown domain errors into unified reporting.
 
-2. **Phase 2: Smart detection and missing-tool policy**
-   - Implement relevance vs availability model.
-   - Apply optional-tool skip semantics by default.
-   - Align multi-tsconfig target derivation with parser project configuration.
-   - Fix include-pattern normalization so extension-bearing entries remain valid.
+2. **Phase 2: Smart detection and missing-tool policy** *(complete)*
+   - Implemented relevance vs availability model.
+   - Applied optional-tool skip semantics by default.
+   - Aligned multi-tsconfig target derivation with parser project configuration (lint targets and ESLint parser projects now share the canonical tsconfig set).
+   - Fixed include-pattern normalization so extension-bearing entries remain valid.
 
 3. **Phase 3: New CLI for domain selection**
    - Add `--domain`, `--skip-domain`, `--list-domains`, `--explain`.
@@ -420,7 +405,7 @@ Notes:
    - Continue supporting v1 config as a subset mapping to the eslint domain.
 
 5. **Phase 5: Extension point hardening**
-   - Stabilize a plugin loading mechanism and document the domain plugin API.
+   - Stabilize built-in domain extension surfaces and document downstream ESLint composition guidance.
    - Expand CI matrix/scenarios to cover domain-only invocations not exercised by current repo scripts.
 
 ### Risks and mitigations
diff --git a/plans/refactor/STATE.md b/plans/refactor/STATE.md
index 122f93d..f6f31bc 100644
--- a/plans/refactor/STATE.md
+++ b/plans/refactor/STATE.md
@@ -4,6 +4,7 @@
 
 - First implementation slice for CLI execution semantics has been delivered.
 - The target architecture is described in [`PLAN.md`](PLAN.md).
+- Multi-tsconfig targeting alignment is complete; lint target derivation and ESLint parser projects now share the same canonical tsconfig set.
 
 ## Implemented in full multi-tsconfig targeting alignment slice
 
@@ -22,7 +23,7 @@
   - only extensionless include entries are expanded with supported ESLint extensions
   - malformed glob synthesis paths from blanket suffixing are eliminated
 - Completed parser-project/target alignment across ESLint runtime paths:
-  - [`src/configs/js.ts`](../../src/configs/js.ts) continues to source parser project from resolved tsconfig list
+  - [`src/configs/eslint.ts`](../../src/configs/eslint.ts) continues to source parser project from resolved tsconfig list
   - [`src/utils.ts`](../../src/utils.ts) now injects parser `project` override from the same resolved config used for target derivation
   - [`src/domains/eslint.ts`](../../src/domains/eslint.ts) detection now derives default scope from the same multi-tsconfig union logic
 - Added regression coverage for multi-tsconfig alignment:
@@ -38,10 +39,10 @@
   - normalized output provides a single resolved shape for CLI/engine consumers
 - Updated runtime consumers to use the dedicated config module:
   - [`src/utils.ts`](../../src/utils.ts)
-  - [`src/configs/js.ts`](../../src/configs/js.ts)
+  - [`src/configs/eslint.ts`](../../src/configs/eslint.ts)
 - Expanded public exports for coherent extensibility:
   - [`package.json`](../../package.json) includes `./configs/*.js` typed/import exports
-  - canonical downstream preset import is `@matrixai/lint/configs/js.js`
+  - canonical downstream preset import is `@matrixai/lint/configs/eslint.js`
   - reusable downstream config import path available for `@matrixai/lint/configs/prettier.config.js`
 - Updated tests and docs for the new boundary:
   - adjusted programmatic export test in [`tests/index.test.ts`](../../tests/index.test.ts)
@@ -149,7 +150,7 @@
 - Implemented changes:
   - replaced [`src/configs/prettier.config.mjs`](../../src/configs/prettier.config.mjs) with [`src/configs/prettier.config.js`](../../src/configs/prettier.config.js)
   - updated imports and runtime references in:
-    - [`src/configs/js.ts`](../../src/configs/js.ts)
+    - [`src/configs/eslint.ts`](../../src/configs/eslint.ts)
     - [`src/bin/lint.ts`](../../src/bin/lint.ts)
 - Rationale:
   - the file is consumed directly at runtime by both ESLint config composition and Prettier CLI `--config`
@@ -183,7 +184,7 @@ Notes on resolved items:
 
 ## Next actions
 
-- Continue phased implementation from [`PLAN.md`](PLAN.md):
-  - move toward domain/plugin architecture internals
-  - align config evolution with v2 schema and precedence
-  - extend domain coverage and execution diagnostics (`--explain`, registry-style reporting)
+- Final cleanup for release:
+  - polish docs for domain/target selection and public import paths
+  - align scripts to canonical domain-targeting CLI usage
+  - cut release (version bump, build, test, lintfix)
diff --git a/src/configs/js.ts b/src/configs/eslint.ts
similarity index 100%
rename from src/configs/js.ts
rename to src/configs/eslint.ts
diff --git a/src/index.ts b/src/index.ts
index ea67d18..96d5f50 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -1,4 +1,4 @@
-export { default as config } from './configs/js.js';
+export { default as config } from './configs/eslint.js';
 export type {
   CLIOptions,
   LintDomain,
diff --git a/src/utils.ts b/src/utils.ts
index be043b0..93ca929 100644
--- a/src/utils.ts
+++ b/src/utils.ts
@@ -59,7 +59,7 @@ async function runESLint({
   logger: Logger;
 }): Promise<boolean> {
   const dirname = path.dirname(url.fileURLToPath(import.meta.url));
-  const defaultConfigPath = path.resolve(dirname, './configs/js.js');
+  const defaultConfigPath = path.resolve(dirname, './configs/eslint.js');
   const lintConfig = resolvedConfig ?? resolveLintConfig();
   const parserProjectOverride = {
     languageOptions: {
diff --git a/tests/index.test.ts b/tests/index.test.ts
index b1002b5..620b23e 100644
--- a/tests/index.test.ts
+++ b/tests/index.test.ts
@@ -1,4 +1,4 @@
-import eslintConfigDefault from '#configs/js.js';
+import eslintConfigDefault from '#configs/eslint.js';
 import { config } from '#index.js';
 
 describe('index exports', () => {