rulesync 9.6.3 → 9.7.0

package/dist/{import-A1yGuzwv.js → import-DC9T1JlQ.js}

@@ -8,6 +8,7 @@ import { intersection, kebabCase, uniq } from "es-toolkit";
 import { globbySync } from "globby";
 import { isDeepStrictEqual } from "node:util";
 import * as smolToml from "smol-toml";
+import { parse as parse$1, stringify } from "smol-toml";
 import matter from "gray-matter";
 import { YAMLException, dump, load } from "js-yaml";
 import { omit } from "es-toolkit/object";
@@ -2677,6 +2678,13 @@ const CODEXCLI_MCP_FILE_NAME = "config.toml";
 const CODEXCLI_RULE_FILE_NAME = "AGENTS.md";
 const CODEXCLI_BASH_RULES_FILE_NAME = "rulesync.rules";
 const CODEXCLI_OPENAI_YAML_RELATIVE_PATH = join("agents", "openai.yaml");
+const CODEXCLI_OVERRIDE_KEYS = [
+	"approval_policy",
+	"sandbox_mode",
+	"sandbox_workspace_write",
+	"apps",
+	"approvals_reviewer"
+];
 //#endregion
 //#region src/features/commands/codexcli-command.ts
 const CodexcliCommandFrontmatterSchema = z.looseObject({
@@ -4055,14 +4063,22 @@ function sanitizeSharedConfigValue(value) {
 * root follows `invalidRootPolicy`. Syntax errors are wrapped with the file
 * path when one is given.
 */
-function parseSharedConfig({ format, fileContent, filePath, invalidRootPolicy = "coerce-empty" }) {
+function parseSharedConfig({ format, fileContent, filePath, invalidRootPolicy = "coerce-empty", jsoncParseErrors = "tolerate" }) {
 	if (fileContent.trim() === "") return {};
 	const at = filePath === void 0 ? "" : ` at ${filePath}`;
 	let parsed;
 	try {
 		if (format === "yaml") parsed = loadYaml(fileContent);
+		else if (format === "toml") parsed = parse$1(fileContent);
 		else if (format === "json") parsed = JSON.parse(fileContent);
-		else parsed = parse(fileContent);
+		else if (jsoncParseErrors === "error") {
+			const errors = [];
+			parsed = parse(fileContent, errors, { allowTrailingComma: true });
+			if (errors.length > 0) {
+				const details = errors.map((error) => `${printParseErrorCode(error.error)} at offset ${error.offset}`).join(", ");
+				throw new Error(details);
+			}
+		} else parsed = parse(fileContent);
 	} catch (error) {
 		throw new Error(`Failed to parse shared config${at}: ${formatError(error)}`, { cause: error });
 	}
@@ -4076,13 +4092,15 @@ function parseSharedConfig({ format, fileContent, filePath, invalidRootPolicy =
 /**
 * Serialize a shared config document. YAML output always ends with exactly one
 * newline; JSON output matches the 2-space `JSON.stringify` shape the JSON
-* writers have always emitted (no trailing newline).
+* writers have always emitted (no trailing newline); TOML output matches the
+* `smol-toml` `stringify` shape the TOML writers have always emitted.
 */
 function stringifySharedConfig({ format, document }) {
 	if (format === "yaml") return dump(document, {
 		noRefs: true,
 		sortKeys: false
 	}).trimEnd() + "\n";
+	if (format === "toml") return stringify(document);
 	return JSON.stringify(document, null, 2);
 }
 /**
@@ -4121,6 +4139,25 @@ function mergeSharedConfigDeep({ base, patch }) {
 const CLAUDE_SETTINGS_SHARED_FILE_KEY = ".claude/settings.json";
 const HERMES_CONFIG_SHARED_FILE_KEY = ".hermes/config.yaml";
 const TAKT_CONFIG_SHARED_FILE_KEY = ".takt/config.yaml";
+const CODEXCLI_CONFIG_SHARED_FILE_KEY = ".codex/config.toml";
+const GROKCLI_CONFIG_SHARED_FILE_KEY = ".grok/config.toml";
+const VIBE_CONFIG_SHARED_FILE_KEY = ".vibe/config.toml";
+const REASONIX_PROJECT_CONFIG_SHARED_FILE_KEY = "reasonix.toml";
+const REASONIX_GLOBAL_CONFIG_SHARED_FILE_KEY = ".reasonix/config.toml";
+/**
+* Build the `SHARED_CONFIG_OWNERSHIP` lookup key from a tool's settable paths.
+* Mirrors `sharedFileKey` in `src/lib/shared-file-derive.ts` (kept separate so
+* feature classes don't pull the processor registry through this module and
+* create an import cycle); the ownership lock-step test keeps the two aligned.
+* Lets a tool whose file lives at a scope-dependent path (`.zed/settings.json`
+* vs `.config/zed/settings.json`) resolve its declaration from the settable
+* paths it already holds.
+*/
+const sharedConfigFileKey = ({ relativeDirPath, relativeFilePath }) => {
+	const dir = relativeDirPath.replace(/\\/g, "/").replace(/\/$/, "");
+	const file = relativeFilePath.replace(/\\/g, "/");
+	return dir === "" || dir === "." ? file : `${dir}/${file}`;
+};
 /**
 * Who owns what in each gateway-managed shared config file, and which policy
 * resolves conflicts. Keys are `dir/file` tokens matching
@@ -4177,6 +4214,298 @@ const SHARED_CONFIG_OWNERSHIP = {
 			},
 			permissions: { kind: "deep-merge" }
 		}
+	},
+	".zed/settings.json": {
+		format: "json",
+		features: {
+			ignore: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["private_files"]
+			},
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["context_servers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["agent"]
+			}
+		}
+	},
+	".config/zed/settings.json": {
+		format: "json",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["context_servers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["agent"]
+			}
+		}
+	},
+	".qwen/settings.json": {
+		format: "json",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcpServers"]
+			},
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["hooks", "disableAllHooks"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"permissions",
+					"tools",
+					"security"
+				]
+			}
+		}
+	},
+	".augment/settings.json": {
+		format: "json",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcpServers"]
+			},
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["hooks"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["toolPermissions"]
+			}
+		}
+	},
+	".devin/config.json": {
+		format: "json",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcpServers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["permissions"]
+			}
+		}
+	},
+	".config/devin/config.json": {
+		format: "json",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcpServers"]
+			},
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["hooks"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["permissions"]
+			}
+		}
+	},
+	".kiro/agents/default.json": {
+		format: "json",
+		features: {
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["hooks"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["allowedTools", "toolsSettings"]
+			}
+		}
+	},
+	".amp/settings.json": {
+		format: "jsonc",
+		invalidRootPolicy: "error",
+		jsoncParseErrors: "error",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["amp.mcpServers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"amp.tools.disable",
+					"amp.permissions",
+					"amp.guardedFiles.allowlist",
+					"amp.dangerouslyAllowAll",
+					"amp.mcpPermissions"
+				]
+			}
+		}
+	},
+	".config/amp/settings.json": {
+		format: "jsonc",
+		invalidRootPolicy: "error",
+		jsoncParseErrors: "error",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["amp.mcpServers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"amp.tools.disable",
+					"amp.permissions",
+					"amp.guardedFiles.allowlist",
+					"amp.dangerouslyAllowAll",
+					"amp.mcpPermissions"
+				]
+			}
+		}
+	},
+	"opencode.json": {
+		format: "jsonc",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp", "tools"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["permission"]
+			},
+			rules: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["instructions"]
+			}
+		}
+	},
+	".config/opencode/opencode.json": {
+		format: "jsonc",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp", "tools"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["permission"]
+			}
+		}
+	},
+	"kilo.json": {
+		format: "jsonc",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp", "tools"]
+			},
+			rules: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["instructions"]
+			}
+		}
+	},
+	".config/kilo/kilo.json": {
+		format: "jsonc",
+		features: { mcp: {
+			kind: "replace-owned-keys",
+			ownedKeys: ["mcp", "tools"]
+		} }
+	},
+	[CODEXCLI_CONFIG_SHARED_FILE_KEY]: {
+		format: "toml",
+		features: {
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["features"]
+			},
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp_servers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"permissions",
+					"default_permissions",
+					...CODEXCLI_OVERRIDE_KEYS
+				]
+			}
+		}
+	},
+	[GROKCLI_CONFIG_SHARED_FILE_KEY]: {
+		format: "toml",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp_servers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["permission", "ui"]
+			}
+		}
+	},
+	[VIBE_CONFIG_SHARED_FILE_KEY]: {
+		format: "toml",
+		features: {
+			hooks: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["enable_experimental_hooks"]
+			},
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["mcp_servers"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"tools",
+					"enabled_tools",
+					"disabled_tools"
+				]
+			}
+		}
+	},
+	[REASONIX_PROJECT_CONFIG_SHARED_FILE_KEY]: {
+		format: "toml",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["plugins"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"permissions",
+					"sandbox",
+					"agent"
+				]
+			}
+		}
+	},
+	[REASONIX_GLOBAL_CONFIG_SHARED_FILE_KEY]: {
+		format: "toml",
+		features: {
+			mcp: {
+				kind: "replace-owned-keys",
+				ownedKeys: ["plugins"]
+			},
+			permissions: {
+				kind: "replace-owned-keys",
+				ownedKeys: [
+					"permissions",
+					"sandbox",
+					"agent"
+				]
+			}
+		}
 	}
 };
 /**
@@ -4197,17 +4526,20 @@ function applySharedConfigPatch({ fileKey, feature, existingContent, patch, file
 		format: declaration.format,
 		fileContent: existingContent,
 		filePath,
-		...declaration.invalidRootPolicy !== void 0 && { invalidRootPolicy: declaration.invalidRootPolicy }
+		...declaration.invalidRootPolicy !== void 0 && { invalidRootPolicy: declaration.invalidRootPolicy },
+		...declaration.jsoncParseErrors !== void 0 && { jsoncParseErrors: declaration.jsoncParseErrors }
 	});
 	if (policy.kind === "replace-owned-keys") {
 		const unowned = Object.keys(patch).filter((key) => !policy.ownedKeys.includes(key));
 		if (unowned.length > 0) throw new Error(`Feature '${feature}' tried to write undeclared keys [${unowned.join(", ")}] to '${fileKey}'; extend its ownedKeys declaration if that ownership is intended.`);
+		const document = mergeSharedConfigShallow({
+			base,
+			patch
+		});
+		for (const [key, value] of Object.entries(patch)) if (value === void 0) delete document[key];
 		return stringifySharedConfig({
 			format: declaration.format,
-			document: mergeSharedConfigShallow({
-				base,
-				patch
-			})
+			document
 		});
 	}
 	const merged = mergeSharedConfigDeep({
@@ -7280,12 +7612,6 @@ var AugmentcodeHooks = class AugmentcodeHooks extends ToolHooks {
 		const paths = AugmentcodeHooks.getSettablePaths({ global });
 		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
 		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
-		let settings;
-		try {
-			settings = JSON.parse(existingContent);
-		} catch (error) {
-			throw new Error(`Failed to parse existing AugmentCode settings at ${filePath}: ${formatError(error)}`, { cause: error });
-		}
 		const config = rulesyncHooks.getJson();
 		const augmentHooks = canonicalToToolHooks({
 			config,
@@ -7293,11 +7619,13 @@ var AugmentcodeHooks = class AugmentcodeHooks extends ToolHooks {
 			converterConfig: AUGMENTCODE_CONVERTER_CONFIG,
 			logger
 		});
-		const merged = {
-			...settings,
-			hooks: augmentHooks
-		};
-		const fileContent = JSON.stringify(merged, null, 2);
+		const fileContent = applySharedConfigPatch({
+			fileKey: sharedConfigFileKey(paths),
+			feature: "hooks",
+			existingContent,
+			patch: { hooks: augmentHooks },
+			filePath
+		});
 		return new AugmentcodeHooks({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
@@ -7464,15 +7792,28 @@ const CODEXCLI_CONVERTER_CONFIG = {
 */
 async function buildCodexConfigTomlContent({ outputRoot }) {
 	const configPath = join(outputRoot, CODEXCLI_DIR, CODEXCLI_MCP_FILE_NAME);
-	const existingContent = await readFileContentOrNull(configPath) ?? smolToml.stringify({});
+	const existingContent = await readFileContentOrNull(configPath) ?? "";
 	let configToml;
 	try {
-		configToml = smolToml.parse(existingContent);
+		configToml = smolToml.parse(existingContent || smolToml.stringify({}));
 	} catch (error) {
 		throw new Error(`Failed to parse existing Codex CLI config at ${configPath}: ${formatError(error)}`, { cause: error });
 	}
-	if (typeof configToml.features === "object" && configToml.features !== null) delete configToml.features.codex_hooks;
-	return smolToml.stringify(configToml);
+	let features;
+	if (typeof configToml.features === "object" && configToml.features !== null) {
+		features = { ...configToml.features };
+		delete features.codex_hooks;
+	}
+	return applySharedConfigPatch({
+		fileKey: sharedConfigFileKey({
+			relativeDirPath: CODEXCLI_DIR,
+			relativeFilePath: CODEXCLI_MCP_FILE_NAME
+		}),
+		feature: "hooks",
+		existingContent,
+		patch: { features },
+		filePath: configPath
+	});
 }
 /**
 * Represents the `.codex/config.toml` file as a generated ToolFile,
@@ -8388,17 +8729,13 @@ var DevinHooks = class DevinHooks extends ToolHooks {
 		let fileContent;
 		if (global) {
 			const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
-			let parsedSettings;
-			try {
-				parsedSettings = JSON.parse(existingContent);
-			} catch (error) {
-				throw new Error(`Failed to parse existing Devin config at ${filePath}: ${formatError(error)}`, { cause: error });
-			}
-			const merged = {
-				...isRecord(parsedSettings) ? parsedSettings : {},
-				hooks: devinHooks
-			};
-			fileContent = JSON.stringify(merged, null, 2);
+			fileContent = applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "hooks",
+				existingContent,
+				patch: { hooks: devinHooks },
+				filePath
+			});
 		} else {
 			await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
 			fileContent = JSON.stringify(devinHooks, null, 2);
@@ -9210,18 +9547,14 @@ var KiroHooks = class KiroHooks extends ToolHooks {
 		const paths = KiroHooks.getSettablePaths({ global });
 		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
 		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
-		let agentConfig;
-		try {
-			agentConfig = JSON.parse(existingContent);
-		} catch (error) {
-			throw new Error(`Failed to parse existing Kiro agent config at ${filePath}: ${formatError(error)}`, { cause: error });
-		}
 		const kiroHooks = canonicalToKiroHooks(rulesyncHooks.getJson(), this.getOverrideKey());
-		const merged = {
-			...agentConfig,
-			hooks: kiroHooks
-		};
-		const fileContent = JSON.stringify(merged, null, 2);
+		const fileContent = applySharedConfigPatch({
+			fileKey: sharedConfigFileKey(paths),
+			feature: "hooks",
+			existingContent,
+			patch: { hooks: kiroHooks },
+			filePath
+		});
 		return new KiroHooks({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
@@ -9716,21 +10049,17 @@ var QwencodeHooks = class QwencodeHooks extends ToolHooks {
 		const paths = QwencodeHooks.getSettablePaths({ global });
 		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
 		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
-		let settings;
-		try {
-			settings = JSON.parse(existingContent);
-		} catch (error) {
-			throw new Error(`Failed to parse existing Qwen Code settings at ${filePath}: ${formatError(error)}`, { cause: error });
-		}
 		const config = rulesyncHooks.getJson();
-		const qwencodeHooks = canonicalToQwencodeHooks(config);
-		const merged = {
-			...settings,
-			hooks: qwencodeHooks
-		};
+		const patch = { hooks: canonicalToQwencodeHooks(config) };
 		const disableAllHooks = config.qwencode?.disableAllHooks;
-		if (typeof disableAllHooks === "boolean") merged.disableAllHooks = disableAllHooks;
-		const fileContent = JSON.stringify(merged, null, 2);
+		if (typeof disableAllHooks === "boolean") patch.disableAllHooks = disableAllHooks;
+		const fileContent = applySharedConfigPatch({
+			fileKey: sharedConfigFileKey(paths),
+			feature: "hooks",
+			existingContent,
+			patch,
+			filePath
+		});
 		return new QwencodeHooks({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
@@ -9989,10 +10318,6 @@ function canonicalToVibeHooks(config, toolOverride) {
 	}
 	return { hooks };
 }
-/**
-* Reverse {@link canonicalToVibeHooks}: parse the flat `[[hooks]]` array back
-* into a canonical event → definition[] record.
-*/
 /** Convert one raw `[[hooks]]` entry to a canonical definition, or null to skip. */
 function vibeEntryToCanonicalDef(raw) {
 	if (raw === null || typeof raw !== "object" || Array.isArray(raw)) return null;
@@ -10012,6 +10337,10 @@ function vibeEntryToCanonicalDef(raw) {
 		def
 	};
 }
+/**
+* Reverse {@link canonicalToVibeHooks}: parse the flat `[[hooks]]` array back
+* into a canonical event → definition[] record.
+*/
 function vibeHooksToCanonical(parsed) {
 	const canonical = {};
 	if (parsed === null || typeof parsed !== "object" || Array.isArray(parsed)) return canonical;
@@ -10040,15 +10369,22 @@ function parseVibeToml(fileContent) {
 */
 async function buildVibeConfigTomlContent({ outputRoot }) {
 	const configPath = join(outputRoot, VIBE_DIR, VIBE_CONFIG_FILE_NAME);
-	const existingContent = await readFileContentOrNull(configPath) ?? smolToml.stringify({});
-	let config;
+	const existingContent = await readFileContentOrNull(configPath) ?? "";
 	try {
-		config = parseVibeToml(existingContent);
+		parseVibeToml(existingContent);
 	} catch (error) {
 		throw new Error(`Failed to parse existing Vibe config at ${configPath}: ${formatError(error)}`, { cause: error });
 	}
-	config.enable_experimental_hooks = true;
-	return smolToml.stringify(config);
+	return applySharedConfigPatch({
+		fileKey: sharedConfigFileKey({
+			relativeDirPath: VIBE_DIR,
+			relativeFilePath: VIBE_CONFIG_FILE_NAME
+		}),
+		feature: "hooks",
+		existingContent,
+		patch: { enable_experimental_hooks: true },
+		filePath: configPath
+	});
 }
 /**
 * Represents the `.vibe/config.toml` file as a generated ToolFile so it goes
@@ -11548,17 +11884,18 @@ var ZedIgnore = class ZedIgnore extends ToolIgnore {
 		const patterns = rulesyncIgnore.getFileContent().split(/\r?\n|\r/).map((line) => line.trim()).filter((line) => line.length > 0 && !line.startsWith("#"));
 		const filePath = join(outputRoot, this.getSettablePaths().relativeDirPath, this.getSettablePaths().relativeFilePath);
 		const existingFileContent = await fileExists(filePath) ? await readFileContent(filePath) : "{}";
-		const existingJsonValue = JSON.parse(existingFileContent);
-		const mergedPatterns = uniq([...existingJsonValue.private_files ?? [], ...patterns].toSorted());
-		const jsonValue = {
-			...existingJsonValue,
-			private_files: mergedPatterns
-		};
+		const mergedPatterns = uniq([...JSON.parse(existingFileContent).private_files ?? [], ...patterns].toSorted());
 		return new ZedIgnore({
 			outputRoot,
 			relativeDirPath: this.getSettablePaths().relativeDirPath,
 			relativeFilePath: this.getSettablePaths().relativeFilePath,
-			fileContent: JSON.stringify(jsonValue, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(this.getSettablePaths()),
+				feature: "ignore",
+				existingContent: existingFileContent,
+				patch: { private_files: mergedPatterns },
+				filePath
+			}),
 			validate: true
 		});
 	}
@@ -12015,17 +12352,17 @@ var AmpMcp = class AmpMcp extends ToolMcp {
 		const basePaths = this.getSettablePaths({ global });
 		const jsonDir = join(outputRoot, basePaths.relativeDirPath);
 		const { fileContent, relativeFilePath } = await this.resolveSettingsFile(jsonDir);
-		const json = fileContent ? parseAmpSettingsJsonc(fileContent) : { [AMP_MCP_SERVERS_KEY]: {} };
-		const filteredMcpServers = filterMcpServers(rulesyncMcp.getMcpServers());
-		const newJson = {
-			...json,
-			[AMP_MCP_SERVERS_KEY]: filteredMcpServers
-		};
 		return new AmpMcp({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "mcp",
+				existingContent: fileContent ?? "",
+				patch: { [AMP_MCP_SERVERS_KEY]: filterMcpServers(rulesyncMcp.getMcpServers()) },
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate,
 			global
 		});
@@ -12312,15 +12649,19 @@ var AugmentcodeMcp = class AugmentcodeMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const merged = {
-			...parseAugmentcodeSettings(await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), JSON.stringify({}, null, 2)), paths.relativeDirPath, paths.relativeFilePath),
-			mcpServers: rulesyncMcp.getMcpServers()
-		};
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({}, null, 2));
 		return new AugmentcodeMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(merged, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { mcpServers: rulesyncMcp.getMcpServers() },
+				filePath
+			}),
 			validate,
 			global
 		});
@@ -12714,8 +13055,9 @@ var CodexcliMcp = class CodexcliMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const configTomlFileContent = await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), smolToml.stringify({}));
-		const configToml = smolToml.parse(configTomlFileContent);
+		const configTomlFilePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const configTomlFileContent = await readFileContentOrNull(configTomlFilePath) ?? "";
+		const configToml = smolToml.parse(configTomlFileContent || smolToml.stringify({}));
 		const strippedMcpServers = rulesyncMcp.getMcpServers();
 		const rawMcpServers = rulesyncMcp.getJson().mcpServers;
 		const converted = convertToCodexFormat(Object.fromEntries(Object.entries(strippedMcpServers).map(([serverName, serverConfig]) => {
@@ -12728,7 +13070,7 @@ var CodexcliMcp = class CodexcliMcp extends ToolMcp {
 		const filteredMcpServers = this.removeEmptyEntries(converted);
 		for (const name of Object.keys(converted)) if (!Object.hasOwn(filteredMcpServers, name)) warnWithFallback(void 0, `MCP server "${name}" had no non-empty configuration and was dropped from the codex CLI config`);
 		const existingMcpServers = isRecord(configToml["mcp_servers"]) ? configToml["mcp_servers"] : {};
-		configToml["mcp_servers"] = Object.fromEntries(Object.entries(filteredMcpServers).map(([name, serverConfig]) => {
+		const mergedMcpServers = Object.fromEntries(Object.entries(filteredMcpServers).map(([name, serverConfig]) => {
 			const existingServer = isRecord(existingMcpServers[name]) ? existingMcpServers[name] : void 0;
 			const serverRecord = serverConfig;
 			if (existingServer && isRecord(existingServer["tools"]) && !("tools" in serverRecord)) return [name, {
@@ -12741,7 +13083,13 @@ var CodexcliMcp = class CodexcliMcp extends ToolMcp {
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(configToml),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent: configTomlFileContent,
+				patch: { mcp_servers: mergedMcpServers },
+				filePath: configTomlFilePath
+			}),
 			validate
 		});
 	}
@@ -13308,16 +13656,19 @@ var DevinMcp = class DevinMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const fileContent = await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), JSON.stringify({ mcpServers: {} }, null, 2));
-		const devinConfig = {
-			...this.parseJsonOrThrow(fileContent, paths.relativeDirPath, paths.relativeFilePath),
-			mcpServers: rulesyncMcp.getMcpServers()
-		};
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({ mcpServers: {} }, null, 2));
 		return new DevinMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(devinConfig, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { mcpServers: rulesyncMcp.getMcpServers() },
+				filePath
+			}),
 			validate,
 			global
 		});
@@ -13804,17 +14155,22 @@ var GrokcliMcp = class GrokcliMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const configTomlFileContent = await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), smolToml.stringify({}));
-		const configToml = smolToml.parse(configTomlFileContent);
+		const configTomlFilePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const configTomlFileContent = await readFileContentOrNull(configTomlFilePath) ?? "";
 		const converted = convertToGrokFormat(rulesyncMcp.getMcpServers());
 		const filteredMcpServers = this.removeEmptyEntries(converted);
 		for (const name of Object.keys(converted)) if (!Object.hasOwn(filteredMcpServers, name)) warnWithFallback(void 0, `MCP server "${name}" had no non-empty configuration and was dropped from the grok CLI config`);
-		configToml["mcp_servers"] = filteredMcpServers;
 		return new GrokcliMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(configToml),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent: configTomlFileContent,
+				patch: { mcp_servers: filteredMcpServers },
+				filePath: configTomlFilePath
+			}),
 			validate
 		});
 	}
@@ -14347,20 +14703,21 @@ var KiloMcp = class KiloMcp extends ToolMcp {
 			fileContent = await readFileContentOrNull(jsonPath);
 			if (fileContent) relativeFilePath = KILO_JSON_FILE_NAME;
 		}
-		if (!fileContent) fileContent = JSON.stringify({ mcp: {} }, null, 2);
-		const json = parse(fileContent);
 		const { mcp: convertedMcp, tools: mcpTools } = convertToKiloFormat(rulesyncMcp.getMcpServers());
-		const { tools: _existingTools, ...jsonWithoutTools } = json;
-		const newJson = {
-			...jsonWithoutTools,
-			mcp: convertedMcp,
-			...Object.keys(mcpTools).length > 0 && { tools: mcpTools }
-		};
 		return new KiloMcp({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "mcp",
+				existingContent: fileContent ?? "",
+				patch: {
+					mcp: convertedMcp,
+					tools: Object.keys(mcpTools).length > 0 ? mcpTools : void 0
+				},
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate
 		});
 	}
@@ -14389,15 +14746,17 @@ var KiloMcp = class KiloMcp extends ToolMcp {
 		const json = fileContent ? parse(fileContent) : {};
 		const existingInstructions = Array.isArray(json.instructions) ? json.instructions.filter((entry) => typeof entry === "string") : [];
 		const mergedInstructions = Array.from(/* @__PURE__ */ new Set([...existingInstructions, ...instructions])).toSorted();
-		const newJson = {
-			...json,
-			instructions: mergedInstructions
-		};
 		return new KiloMcp({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "rules",
+				existingContent: fileContent ?? "",
+				patch: { instructions: mergedInstructions },
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate
 		});
 	}
@@ -14669,23 +15028,24 @@ var OpencodeMcp = class OpencodeMcp extends ToolMcp {
 			fileContent = await readFileContentOrNull(jsonPath);
 			if (fileContent) relativeFilePath = OPENCODE_JSON_FILE_NAME;
 		}
-		if (!fileContent) fileContent = JSON.stringify({ mcp: {} }, null, 2);
-		const json = parse(fileContent);
 		const { mcp: convertedMcp, tools: mcpTools } = convertToOpencodeFormat(convertEnvVarRefsToToolFormat({
 			mcpServers: rulesyncMcp.getMcpServers(),
 			replacement: "{env:$1}"
 		}));
-		const { tools: _existingTools, ...jsonWithoutTools } = json;
-		const newJson = {
-			...jsonWithoutTools,
-			mcp: convertedMcp,
-			...Object.keys(mcpTools).length > 0 && { tools: mcpTools }
-		};
 		return new OpencodeMcp({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "mcp",
+				existingContent: fileContent ?? "",
+				patch: {
+					mcp: convertedMcp,
+					tools: Object.keys(mcpTools).length > 0 ? mcpTools : void 0
+				},
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate
 		});
 	}
@@ -14720,15 +15080,17 @@ var OpencodeMcp = class OpencodeMcp extends ToolMcp {
 		const json = fileContent ? parse(fileContent) : {};
 		const existingInstructions = Array.isArray(json.instructions) ? json.instructions.filter((entry) => typeof entry === "string") : [];
 		const mergedInstructions = Array.from(/* @__PURE__ */ new Set([...existingInstructions, ...instructions])).toSorted();
-		const newJson = {
-			...json,
-			instructions: mergedInstructions
-		};
 		return new OpencodeMcp({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "rules",
+				existingContent: fileContent ?? "",
+				patch: { instructions: mergedInstructions },
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate
 		});
 	}
@@ -14838,16 +15200,19 @@ var QwencodeMcp = class QwencodeMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const fileContent = await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), JSON.stringify({ mcpServers: {} }, null, 2));
-		const newJson = {
-			...JSON.parse(fileContent),
-			mcpServers: convertToQwencodeFormat(rulesyncMcp.getMcpServers())
-		};
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readOrInitializeFileContent(filePath, JSON.stringify({ mcpServers: {} }, null, 2));
 		return new QwencodeMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { mcpServers: convertToQwencodeFormat(rulesyncMcp.getMcpServers()) },
+				filePath
+			}),
 			validate
 		});
 	}
@@ -14932,13 +15297,20 @@ var ReasonixMcp = class ReasonixMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const config = parseReasonixConfig$1(await readFileContentOrNull(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath)) ?? smolToml.stringify({}));
-		config.plugins = Object.entries(rulesyncMcp.getMcpServers()).map(([name, server]) => rulesyncMcpServerToReasonix(name, server));
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readFileContentOrNull(filePath) ?? "";
+		const plugins = Object.entries(rulesyncMcp.getMcpServers()).map(([name, server]) => rulesyncMcpServerToReasonix(name, server));
 		return new ReasonixMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(config),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { plugins },
+				filePath
+			}),
 			validate,
 			global
 		});
@@ -15413,13 +15785,20 @@ var VibeMcp = class VibeMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const config = parseVibeConfig$1(await readFileContentOrNull(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath)) ?? smolToml.stringify({}));
-		config.mcp_servers = Object.entries(rulesyncMcp.getMcpServers()).map(([name, server]) => rulesyncMcpServerToVibe(name, server));
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readFileContentOrNull(filePath) ?? "";
+		const mcpServers = Object.entries(rulesyncMcp.getMcpServers()).map(([name, server]) => rulesyncMcpServerToVibe(name, server));
 		return new VibeMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(config),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { mcp_servers: mcpServers },
+				filePath
+			}),
 			validate,
 			global
 		});
@@ -15650,16 +16029,19 @@ var ZedMcp = class ZedMcp extends ToolMcp {
 	}
 	static async fromRulesyncMcp({ outputRoot = process.cwd(), rulesyncMcp, validate = true, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const fileContent = await readOrInitializeFileContent(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath), "{}");
-		const newJson = {
-			...JSON.parse(fileContent),
-			context_servers: rulesyncMcp.getMcpServers()
-		};
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readOrInitializeFileContent(filePath, "{}");
 		return new ZedMcp({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "mcp",
+				existingContent,
+				patch: { context_servers: rulesyncMcp.getMcpServers() },
+				filePath
+			}),
 			validate
 		});
 	}
@@ -16828,25 +17210,29 @@ var AmpPermissions = class AmpPermissions extends ToolPermissions {
 		const override = config.amp;
 		const authoredExtras = override?.permissions ? toPermissionsList(override.permissions) : [];
 		const preservedDelegates = override?.permissions ? [] : toPermissionsList(json[AMP_PERMISSIONS_KEY]).filter((entry) => entry.action === "delegate");
-		const newJson = {
-			...json,
-			[AMP_TOOLS_DISABLE_KEY]: disable
-		};
 		const mergedPermissions = mergeAmpPermissions([
 			...permissions,
 			...authoredExtras,
 			...preservedDelegates
 		]);
-		if (mergedPermissions.length > 0) newJson[AMP_PERMISSIONS_KEY] = mergedPermissions;
-		else delete newJson[AMP_PERMISSIONS_KEY];
-		if (override?.guardedFiles?.allowlist !== void 0) newJson[AMP_GUARDED_FILES_ALLOWLIST_KEY] = override.guardedFiles.allowlist;
-		if (override?.dangerouslyAllowAll !== void 0) newJson[AMP_DANGEROUSLY_ALLOW_ALL_KEY] = override.dangerouslyAllowAll;
-		if (override?.mcpPermissions !== void 0) newJson[AMP_MCP_PERMISSIONS_KEY] = override.mcpPermissions;
+		const patch = {
+			[AMP_TOOLS_DISABLE_KEY]: disable,
+			[AMP_PERMISSIONS_KEY]: mergedPermissions.length > 0 ? mergedPermissions : void 0
+		};
+		if (override?.guardedFiles?.allowlist !== void 0) patch[AMP_GUARDED_FILES_ALLOWLIST_KEY] = override.guardedFiles.allowlist;
+		if (override?.dangerouslyAllowAll !== void 0) patch[AMP_DANGEROUSLY_ALLOW_ALL_KEY] = override.dangerouslyAllowAll;
+		if (override?.mcpPermissions !== void 0) patch[AMP_MCP_PERMISSIONS_KEY] = override.mcpPermissions;
 		return new AmpPermissions({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(newJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "permissions",
+				existingContent: fileContent ?? "",
+				patch,
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate: true
 		});
 	}
@@ -17788,11 +18174,13 @@ var AugmentcodePermissions = class AugmentcodePermissions extends ToolPermission
 			...preservedBasicEntries,
 			...authoredBasics
 		]);
-		const merged = {
-			...settings,
-			toolPermissions: [...specialEntries, ...sortedBasic]
-		};
-		const fileContent = JSON.stringify(merged, null, 2);
+		const fileContent = applySharedConfigPatch({
+			fileKey: sharedConfigFileKey(paths),
+			feature: "permissions",
+			existingContent,
+			patch: { toolPermissions: [...specialEntries, ...sortedBasic] },
+			filePath
+		});
 		return new AugmentcodePermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
@@ -18384,13 +18772,6 @@ const WORKSPACE_WIDE_WRITE_PATTERNS = /* @__PURE__ */ new Set([
 ]);
 const CODEX_MINIMAL_KEY = ":minimal";
 const GLOBAL_WILDCARD_DOMAIN = "*";
-const CODEXCLI_OVERRIDE_KEYS = [
-	"approval_policy",
-	"sandbox_mode",
-	"sandbox_workspace_write",
-	"apps",
-	"approvals_reviewer"
-];
 var CodexcliPermissions = class CodexcliPermissions extends ToolPermissions {
 	static getSettablePaths(_options = {}) {
 		return {
@@ -18414,26 +18795,27 @@ var CodexcliPermissions = class CodexcliPermissions extends ToolPermissions {
 	}
 	static async fromRulesyncPermissions({ outputRoot = process.cwd(), rulesyncPermissions, validate = true, logger, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const existingContent = await readFileContentOrNull(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath)) ?? smolToml.stringify({});
-		const parsed = toMutableTable(smolToml.parse(existingContent));
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readFileContentOrNull(filePath) ?? "";
+		const existing = toMutableTable(smolToml.parse(existingContent || smolToml.stringify({})));
 		const newProfile = convertRulesyncToCodexProfile({
 			config: rulesyncPermissions.getJson(),
 			logger
 		});
-		const permissionsTable = toMutableTable(parsed.permissions);
+		const permissionsTable = toMutableTable(existing.permissions);
 		const { profile: existingProfile, domainsHadUnknown: existingDomainsHadUnknown } = toCodexProfile(permissionsTable[RULESYNC_PROFILE_NAME]);
-		if (existingProfile?.extends !== void 0 && existingProfile.extends !== newProfile.extends) logger?.warn(`Existing "extends" value "${existingProfile.extends}" will be replaced by Rulesync-managed "${newProfile.extends ?? "(none)"}".`);
-		if (existingProfile?.network?.unix_sockets !== void 0) logger?.warn(`Preserving existing "network.unix_sockets" from config. Review these entries manually as they may grant broad system access.`);
-		if (existingProfile?.network?.mode !== void 0) logger?.warn(`Preserving existing "network.mode" from config. Review this value manually as it may grant broader network access than the Rulesync-managed domain rules.`);
-		if (existingDomainsHadUnknown) logger?.warn(`Existing "network.domains" contained unrecognized values. These entries were skipped and will not be imported.`);
+		warnAboutPreservedProfileState({
+			existingProfile,
+			newProfile,
+			existingDomainsHadUnknown,
+			logger
+		});
 		permissionsTable[RULESYNC_PROFILE_NAME] = mergeWithExistingProfile({
 			newProfile,
 			existingProfile
 		});
-		parsed.permissions = permissionsTable;
-		parsed.default_permissions = RULESYNC_PROFILE_NAME;
-		applyCodexcliOverride({
-			parsed,
+		const overridePatch = computeCodexcliOverridePatch({
+			existing,
 			override: rulesyncPermissions.getJson().codexcli,
 			logger
 		});
@@ -18441,7 +18823,17 @@ var CodexcliPermissions = class CodexcliPermissions extends ToolPermissions {
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(parsed),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: {
+					permissions: permissionsTable,
+					default_permissions: RULESYNC_PROFILE_NAME,
+					...overridePatch
+				},
+				filePath
+			}),
 			validate
 		});
 	}
@@ -18611,6 +19003,12 @@ function toCodexProfile(value) {
 		domainsHadUnknown
 	};
 }
+function warnAboutPreservedProfileState({ existingProfile, newProfile, existingDomainsHadUnknown, logger }) {
+	if (existingProfile?.extends !== void 0 && existingProfile.extends !== newProfile.extends) logger?.warn(`Existing "extends" value "${existingProfile.extends}" will be replaced by Rulesync-managed "${newProfile.extends ?? "(none)"}".`);
+	if (existingProfile?.network?.unix_sockets !== void 0) logger?.warn(`Preserving existing "network.unix_sockets" from config. Review these entries manually as they may grant broad system access.`);
+	if (existingProfile?.network?.mode !== void 0) logger?.warn(`Preserving existing "network.mode" from config. Review this value manually as it may grant broader network access than the Rulesync-managed domain rules.`);
+	if (existingDomainsHadUnknown) logger?.warn(`Existing "network.domains" contained unrecognized values. These entries were skipped and will not be imported.`);
+}
 function mergeWithExistingProfile({ newProfile, existingProfile }) {
 	if (!existingProfile) return newProfile;
 	const mergedNetwork = { ...newProfile.network };
@@ -18661,8 +19059,9 @@ function toMutableTable(value) {
 function isPlainObject(value) {
 	return value !== null && typeof value === "object" && !Array.isArray(value);
 }
-function applyCodexcliOverride({ parsed, override, logger }) {
-	if (!override) return;
+function computeCodexcliOverridePatch({ existing, override, logger }) {
+	const patch = {};
+	if (!override) return patch;
 	const allowed = new Set(CODEXCLI_OVERRIDE_KEYS);
 	for (const [key, value] of Object.entries(override)) {
 		if (!allowed.has(key)) {
@@ -18670,12 +19069,13 @@ function applyCodexcliOverride({ parsed, override, logger }) {
 			continue;
 		}
 		if (value === void 0) continue;
-		const existing = parsed[key];
-		parsed[key] = isPlainObject(existing) && isPlainObject(value) ? {
-			...existing,
+		const existingValue = existing[key];
+		patch[key] = isPlainObject(existingValue) && isPlainObject(value) ? {
+			...existingValue,
 			...value
 		} : value;
 	}
+	return patch;
 }
 function extractCodexcliOverride(table) {
 	const override = {};
@@ -19236,15 +19636,17 @@ var DevinPermissions = class DevinPermissions extends ToolPermissions {
 		else delete mergedPermissions.ask;
 		if (mergedDeny.length > 0) mergedPermissions.deny = mergedDeny;
 		else delete mergedPermissions.deny;
-		const merged = {
-			...settings,
-			permissions: mergedPermissions
-		};
 		return new DevinPermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(merged, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: { permissions: mergedPermissions },
+				filePath
+			}),
 			validate
 		});
 	}
@@ -19853,23 +20255,31 @@ var GrokcliPermissions = class GrokcliPermissions extends ToolPermissions {
 		const config = rulesyncPermissions.getJson();
 		const existingPermission = isRecord(parsed[GROKCLI_PERMISSION_KEY]) ? parsed[GROKCLI_PERMISSION_KEY] : {};
 		const buckets = buildGrokPermissionArrays(config, existingPermission, logger);
-		parsed[GROKCLI_PERMISSION_KEY] = {
+		const permission = {
 			...existingPermission,
 			allow: buckets.allow,
 			deny: buckets.deny,
 			ask: buckets.ask
 		};
 		const mode = deriveGrokPermissionMode(config);
-		const existingUi = isRecord(parsed[GROKCLI_UI_KEY]) ? parsed[GROKCLI_UI_KEY] : {};
-		parsed[GROKCLI_UI_KEY] = {
-			...existingUi,
+		const ui = {
+			...isRecord(parsed[GROKCLI_UI_KEY]) ? parsed[GROKCLI_UI_KEY] : {},
 			[GROKCLI_PERMISSION_MODE_KEY]: mode
 		};
 		return new GrokcliPermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(parsed),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: {
+					[GROKCLI_PERMISSION_KEY]: permission,
+					[GROKCLI_UI_KEY]: ui
+				},
+				filePath
+			}),
 			validate: true,
 			global: true
 		});
@@ -20572,7 +20982,16 @@ var KiroPermissions = class KiroPermissions extends ToolPermissions {
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(next, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: {
+					allowedTools: next.allowedTools,
+					toolsSettings: next.toolsSettings
+				},
+				filePath
+			}),
 			validate
 		});
 	}
@@ -20869,21 +21288,22 @@ var OpencodePermissions = class OpencodePermissions extends ToolPermissions {
 			fileContent = await readFileContentOrNull(jsonPath);
 			if (fileContent) relativeFilePath = OPENCODE_JSON_FILE_NAME;
 		}
-		const parsed = parse(fileContent ?? "{}");
 		const rulesyncJson = rulesyncPermissions.getJson();
 		const overridePermission = rulesyncJson.opencode?.permission ?? {};
-		const nextJson = {
-			...parsed,
-			permission: {
-				...rulesyncJson.permission,
-				...overridePermission
-			}
-		};
 		return new OpencodePermissions({
 			outputRoot,
 			relativeDirPath: basePaths.relativeDirPath,
 			relativeFilePath,
-			fileContent: JSON.stringify(nextJson, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(basePaths),
+				feature: "permissions",
+				existingContent: fileContent ?? "",
+				patch: { permission: {
+					...rulesyncJson.permission,
+					...overridePermission
+				} },
+				filePath: join(jsonDir, relativeFilePath)
+			}),
 			validate: true
 		});
 	}
@@ -21092,20 +21512,23 @@ var QwencodePermissions = class QwencodePermissions extends ToolPermissions {
 		else delete mergedPermissions.ask;
 		if (mergedDeny.length > 0) mergedPermissions.deny = mergedDeny;
 		else delete mergedPermissions.deny;
-		const merged = {
-			...settings,
-			permissions: mergedPermissions
-		};
+		const patch = { permissions: mergedPermissions };
 		const override = config.qwencode;
-		if (override?.tools !== void 0) merged.tools = {
+		if (override?.tools !== void 0) patch.tools = {
 			...asPlainRecord(settings.tools),
 			...asPlainRecord(override.tools)
 		};
-		if (override?.security !== void 0) merged.security = {
+		if (override?.security !== void 0) patch.security = {
 			...asPlainRecord(settings.security),
 			...asPlainRecord(override.security)
 		};
-		const fileContent = JSON.stringify(merged, null, 2);
+		const fileContent = applySharedConfigPatch({
+			fileKey: sharedConfigFileKey(paths),
+			feature: "permissions",
+			existingContent,
+			patch,
+			filePath
+		});
 		return new QwencodePermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
@@ -21340,7 +21763,9 @@ var ReasonixPermissions = class ReasonixPermissions extends ToolPermissions {
 	}
 	static async fromRulesyncPermissions({ outputRoot = process.cwd(), rulesyncPermissions, validate = true, logger, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const parsed = parseReasonixConfig(await readFileContentOrNull(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath)) ?? smolToml.stringify({}));
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readFileContentOrNull(filePath) ?? "";
+		const parsed = parseReasonixConfig(existingContent);
 		const config = rulesyncPermissions.getJson();
 		const { allow, ask, deny } = convertRulesyncToReasonixPermissions(config);
 		const managedToolNames = new Set(Object.keys(config.permission).map((category) => toReasonixToolName(category)));
@@ -21365,25 +21790,27 @@ var ReasonixPermissions = class ReasonixPermissions extends ToolPermissions {
 		else delete mergedPermissions.ask;
 		if (mergedDeny.length > 0) mergedPermissions.deny = mergedDeny;
 		else delete mergedPermissions.deny;
-		const merged = {
-			...parsed,
-			permissions: mergedPermissions
-		};
+		const patch = { permissions: mergedPermissions };
 		const override = config.reasonix;
-		if (override?.sandbox !== void 0) merged.sandbox = {
+		if (override?.sandbox !== void 0) patch.sandbox = {
 			...asReasonixRecord(parsed.sandbox),
 			...asReasonixRecord(override.sandbox)
 		};
-		if (override?.agent !== void 0) merged.agent = {
+		if (override?.agent !== void 0) patch.agent = {
 			...asReasonixRecord(parsed.agent),
 			...asReasonixRecord(override.agent)
 		};
-		const fileContent = smolToml.stringify(merged);
 		return new ReasonixPermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent,
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch,
+				filePath
+			}),
 			validate
 		});
 	}
@@ -21954,7 +22381,9 @@ var VibePermissions = class VibePermissions extends ToolPermissions {
 	}
 	static async fromRulesyncPermissions({ outputRoot = process.cwd(), rulesyncPermissions, validate = true, logger, global = false }) {
 		const paths = this.getSettablePaths({ global });
-		const config = parseVibeConfig(await readFileContentOrNull(join(outputRoot, paths.relativeDirPath, paths.relativeFilePath)) ?? smolToml.stringify({}));
+		const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+		const existingContent = await readFileContentOrNull(filePath) ?? "";
+		const config = parseVibeConfig(existingContent);
 		const permission = rulesyncPermissions.getJson().permission;
 		const tools = toVibeToolsRecord(config.tools);
 		const enabledTools = new Set(toStringArray(config.enabled_tools));
@@ -21999,16 +22428,21 @@ var VibePermissions = class VibePermissions extends ToolPermissions {
 			tools[vibeToolName] = nextTool;
 		}
 		applyVibeSensitivePatterns(tools, rulesyncPermissions.getJson().vibe);
-		config.tools = tools;
-		if (enabledTools.size > 0) config.enabled_tools = [...enabledTools].toSorted();
-		else delete config.enabled_tools;
-		if (disabledTools.size > 0) config.disabled_tools = [...disabledTools].toSorted();
-		else delete config.disabled_tools;
 		return new VibePermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: smolToml.stringify(config),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: {
+					tools,
+					enabled_tools: enabledTools.size > 0 ? [...enabledTools].toSorted() : void 0,
+					disabled_tools: disabledTools.size > 0 ? [...disabledTools].toSorted() : void 0
+				},
+				filePath
+			}),
 			validate,
 			global
 		});
@@ -22471,24 +22905,26 @@ var ZedPermissions = class ZedPermissions extends ToolPermissions {
 		}
 		const managedToolNames = new Set(Object.keys(managedTools));
 		const preservedTools = Object.fromEntries(Object.entries(existingTools).filter(([toolName]) => !managedToolNames.has(toolName)));
-		const mergedSettings = {
-			...settings,
-			agent: {
-				...agent,
-				tool_permissions: {
-					...toolPermissions,
-					tools: {
-						...preservedTools,
-						...managedTools
-					}
-				}
-			}
-		};
 		return new ZedPermissions({
 			outputRoot,
 			relativeDirPath: paths.relativeDirPath,
 			relativeFilePath: paths.relativeFilePath,
-			fileContent: JSON.stringify(mergedSettings, null, 2),
+			fileContent: applySharedConfigPatch({
+				fileKey: sharedConfigFileKey(paths),
+				feature: "permissions",
+				existingContent,
+				patch: { agent: {
+					...agent,
+					tool_permissions: {
+						...toolPermissions,
+						tools: {
+							...preservedTools,
+							...managedTools
+						}
+					}
+				} },
+				filePath
+			}),
 			validate: true
 		});
 	}
@@ -38178,8 +38614,13 @@ const collectFactoryPaths = (factory) => [...settablePathsForScope({
 * Derive, from the processor registry, every on-disk file that two or more
 * features read-modify-write. Source of truth the generation step graph's
 * `writesSharedFile` declarations must match.
+*
+* `minWriters: 1` widens the result to single-feature files as well — used to
+* validate `SHARED_CONFIG_OWNERSHIP` declarations for files that route through
+* the gateway without being cross-feature shared (e.g. a global-scope twin
+* only one feature writes).
 */
-const deriveSharedFileWriters = () => {
+const deriveSharedFileWriters = ({ minWriters = 2 } = {}) => {
 	const byKey = /* @__PURE__ */ new Map();
 	const pathByKey = /* @__PURE__ */ new Map();
 	for (const entry of PROCESSOR_REGISTRY) {
@@ -38205,7 +38646,7 @@ const deriveSharedFileWriters = () => {
 	}
 	const writers = [];
 	for (const [key, features] of byKey) {
-		if (features.size < 2) continue;
+		if (features.size < minWriters) continue;
 		const path = pathByKey.get(key);
 		const toolsByFeature = /* @__PURE__ */ new Map();
 		for (const [feature, tools] of features) toolsByFeature.set(feature, [...tools].toSorted());
@@ -39150,4 +39591,4 @@ async function importPermissionsCore(params) {
 //#endregion
 export { removeTempDirectory as $, RulesyncCommand as A, checkPathTraversal as B, RulesyncHooks as C, RULESYNC_RULES_RELATIVE_DIR_PATH as Ct, CLAUDECODE_MEMORIES_DIR_NAME as D, formatError as Dt, CLAUDECODE_LOCAL_RULE_FILE_NAME as E, RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH as Et, findControlCharacter as F, findFilesByGlobs as G, directoryExists as H, ConsoleLogger as I, isSymlink as J, getFileSize as K, JsonLogger as L, stringifyFrontmatter as M, loadYaml as N, CLAUDECODE_SETTINGS_LOCAL_FILE_NAME as O, ALL_FEATURES as Ot, ConfigResolver as P, removeFile as Q, CLIError as R, HooksProcessor as S, RULESYNC_RELATIVE_DIR_PATH as St, CLAUDECODE_DIR as T, RULESYNC_SOURCES_LOCK_RELATIVE_FILE_PATH as Tt, ensureDir as U, createTempDirectory as V, fileExists as W, readFileContent as X, listDirectoryFiles as Y, removeDirectory as Z, RulesyncPermissions as _, RULESYNC_MCP_RELATIVE_FILE_PATH as _t, convertFromTool as a, MAX_FILE_SIZE as at, IgnoreProcessor as b, RULESYNC_PERMISSIONS_FILE_NAME as bt, RulesyncRuleFrontmatterSchema as c, RULESYNC_COMMANDS_RELATIVE_DIR_PATH as ct, RulesyncSubagentFrontmatterSchema as d, RULESYNC_CURATED_SKILLS_RELATIVE_DIR_PATH as dt, toPosixPath as et, SkillsProcessor as f, RULESYNC_HOOKS_FILE_NAME as ft, SKILL_FILE_NAME as g, RULESYNC_MCP_FILE_NAME as gt, RulesyncSkillFrontmatterSchema as h, RULESYNC_LOCAL_CONFIG_RELATIVE_FILE_PATH as ht, getProcessorRegistryEntry as i, ToolTargetSchema as it, RulesyncCommandFrontmatterSchema as j, CLAUDECODE_SKILLS_DIR_PATH as k, ALL_FEATURES_WITH_WILDCARD as kt, SubagentsProcessor as l, RULESYNC_CONFIG_RELATIVE_FILE_PATH as lt, RulesyncSkill as m, RULESYNC_IGNORE_RELATIVE_FILE_PATH as mt, checkRulesyncDirExists as n, ALL_TOOL_TARGETS as nt, RulesProcessor as o, RULESYNC_AIIGNORE_FILE_NAME as ot, getLocalSkillDirNames as p, RULESYNC_HOOKS_RELATIVE_FILE_PATH as pt, getHomeDirectory as q, generate as r, ALL_TOOL_TARGETS_WITH_WILDCARD as rt, RulesyncRule as s, RULESYNC_AIIGNORE_RELATIVE_FILE_PATH as st, importFromTool as t, writeFileContent as tt, RulesyncSubagent as u, RULESYNC_CONFIG_SCHEMA_URL as ut, McpProcessor as v, RULESYNC_MCP_SCHEMA_URL as vt, CommandsProcessor as w, RULESYNC_SKILLS_RELATIVE_DIR_PATH as wt, RulesyncIgnore as x, RULESYNC_PERMISSIONS_RELATIVE_FILE_PATH as xt, RulesyncMcp as y, RULESYNC_OVERVIEW_FILE_NAME as yt, ErrorCodes as z };
 
-//# sourceMappingURL=import-A1yGuzwv.js.map
+//# sourceMappingURL=import-DC9T1JlQ.js.map