feat(coding-agent): added notebook-aware .ipynb edit/read path helpers

- Added `.ipynb` detection and editable-cell conversion utilities, including merge/serialize helpers in `edit/notebook`.
- Rerouted hashline, patch, and replace edit flows, plus read/write paths, through notebook-aware helpers before persistence.
- Removed the dedicated `notebook` tool, its schema flags, renderer, and built-in registration/settings checks.
- Updated notebook read behavior, docs, and tests so `.ipynb` reads return editable `# %%` cells and edits reserialize to JSON.

packages/coding-agent/src/edit/modes/hashline.ts

@@ -52,6 +52,7 @@ import {
 	HL_HASH_CAPTURE_RE_RAW,
 } from "../line-hash";
 import { detectLineEnding, normalizeToLF, restoreLineEndings, stripBom } from "../normalize";
+import { readEditFileText, serializeEditFileText } from "../read-file";
 import type { EditToolDetails, LspBatchRequest } from "../renderer";
 
 // ───────────────────────────────────────────────────────────────────────────
@@ -1656,11 +1657,14 @@ export function splitHashlineInputs(input: string, options: SplitHashlineOptions
 // 13. Diff computation (for streaming preview)
 // ───────────────────────────────────────────────────────────────────────────
 
-async function readHashlineFileText(file: { text(): Promise<string> }, pathText: string): Promise<string> {
+async function readHashlineFileText(
+	_file: { text(): Promise<string> },
+	absolutePath: string,
+	pathText: string,
+): Promise<string> {
 	try {
-		return await file.text();
+		return await readEditFileText(absolutePath, pathText);
 	} catch (error) {
-		if (isEnoent(error)) throw new Error(`File not found: ${pathText}`);
 		const message = error instanceof Error ? error.message : String(error);
 		throw new Error(message || `Unable to read ${pathText}`);
 	}
@@ -1679,7 +1683,7 @@ export async function computeHashlineDiff(
 		const [section] = sections;
 
 		const absolutePath = resolveToCwd(section.path, cwd);
-		const rawContent = await readHashlineFileText(Bun.file(absolutePath), section.path);
+		const rawContent = await readHashlineFileText(Bun.file(absolutePath), absolutePath, section.path);
 		const { text: content } = stripBom(rawContent);
 		const normalized = normalizeToLF(content);
 		const result = applyHashlineEdits(normalized, parseHashline(section.diff), options);
@@ -1699,11 +1703,13 @@ interface ReadHashlineFileResult {
 	rawContent: string;
 }
 
-async function readHashlineFile(absolutePath: string): Promise<ReadHashlineFileResult> {
+async function readHashlineFile(absolutePath: string, pathText: string): Promise<ReadHashlineFileResult> {
 	try {
-		return { exists: true, rawContent: await Bun.file(absolutePath).text() };
+		return { exists: true, rawContent: await readEditFileText(absolutePath, pathText) };
 	} catch (error) {
 		if (isEnoent(error)) return { exists: false, rawContent: "" };
+		if (error instanceof Error && error.message === `File not found: ${pathText}`)
+			return { exists: false, rawContent: "" };
 		throw error;
 	}
 }
@@ -1746,7 +1752,7 @@ async function preflightHashlineSection(options: ExecuteHashlineSingleOptions &
 	const { edits } = parseHashlineWithWarnings(diff);
 	enforcePlanModeWrite(session, sectionPath, { op: "update" });
 
-	const source = await readHashlineFile(absolutePath);
+	const source = await readHashlineFile(absolutePath, sectionPath);
 	if (!source.exists && hasAnchorScopedEdit(edits)) throw new Error(`File not found: ${sectionPath}`);
 	if (source.exists) assertEditableFileContent(source.rawContent, sectionPath);
 
@@ -1773,7 +1779,7 @@ async function executeHashlineSection(
 	const { edits, warnings: parseWarnings } = parseHashlineWithWarnings(diff);
 	enforcePlanModeWrite(session, sourcePath, { op: "update" });
 
-	const source = await readHashlineFile(absolutePath);
+	const source = await readHashlineFile(absolutePath, sourcePath);
 	if (!source.exists && hasAnchorScopedEdit(edits)) throw new Error(`File not found: ${sourcePath}`);
 	if (source.exists) assertEditableFileContent(source.rawContent, sourcePath);
 
@@ -1789,7 +1795,11 @@ async function executeHashlineSection(
 		};
 	}
 
-	const finalContent = bom + restoreLineEndings(result.lines, originalEnding);
+	const finalContent = await serializeEditFileText(
+		absolutePath,
+		sourcePath,
+		bom + restoreLineEndings(result.lines, originalEnding),
+	);
 	const diagnostics = await writethrough(
 		absolutePath,
 		finalContent,

packages/coding-agent/src/edit/modes/patch.ts

@@ -44,6 +44,7 @@ import {
 	restoreLineEndings,
 	stripBom,
 } from "../normalize";
+import { readEditFileText, serializeEditFileText } from "../read-file";
 import type { EditToolDetails, LspBatchRequest } from "../renderer";
 import {
 	type ContextLineResult,
@@ -104,13 +105,13 @@ export const defaultFileSystem: FileSystem = {
 		return Bun.file(path).exists();
 	},
 	async read(path: string): Promise<string> {
-		return Bun.file(path).text();
+		return readEditFileText(path, path);
 	},
 	async readBinary(path: string): Promise<Uint8Array> {
 		return fs.promises.readFile(path);
 	},
 	async write(path: string, content: string): Promise<void> {
-		await Bun.write(path, content);
+		await Bun.write(path, await serializeEditFileText(path, path, content));
 	},
 	async delete(path: string): Promise<void> {
 		await fs.promises.unlink(path);
@@ -1637,7 +1638,7 @@ class LspFileSystem implements FileSystem {
 	}
 
 	async read(path: string): Promise<string> {
-		return this.#getFile(path).text();
+		return readEditFileText(path, path);
 	}
 
 	async readBinary(path: string): Promise<Uint8Array> {
@@ -1647,10 +1648,11 @@ class LspFileSystem implements FileSystem {
 
 	async write(path: string, content: string): Promise<void> {
 		const file = this.#getFile(path);
+		const finalContent = await serializeEditFileText(path, path, content);
 		const deferredForPath = this.deferredForPath;
 		const result = await this.writethrough(
 			path,
-			content,
+			finalContent,
 			this.signal,
 			file,
 			this.batchRequest,

packages/coding-agent/src/edit/modes/replace.ts

@@ -21,7 +21,7 @@ import {
 	restoreLineEndings,
 	stripBom,
 } from "../normalize";
-import { readEditFileText } from "../read-file";
+import { readEditFileText, serializeEditFileText } from "../read-file";
 import type { EditToolDetails, LspBatchRequest } from "../renderer";
 
 export interface FuzzyMatch {
@@ -1065,7 +1065,11 @@ export async function executeReplaceSingle(
 		throw new Error(`Edits to ${path} resulted in no changes being made.`);
 	}
 
-	const finalContent = bom + restoreLineEndings(result.content, originalEnding);
+	const finalContent = await serializeEditFileText(
+		absolutePath,
+		path,
+		bom + restoreLineEndings(result.content, originalEnding),
+	);
 	const diagnostics = await writethrough(
 		absolutePath,
 		finalContent,