one-code-extension 0.4.0 → 0.5.0

package/extensions/doctor/compat.ts

@@ -8,7 +8,7 @@
  * borrows) and the keys it leaves alone. "Leaves alone" is stated per file
  * because the answer differs by scope on purpose — a repository's own
  * `.claude/settings.json` may not grant itself `auto` mode or configure the
- * auto-mode classifier (docs/decisions/modes.md, auto-mode.md) — and a user
+ * auto-mode classifier (working-docs/decisions/modes.md, auto-mode.md) — and a user
  * reading "works unchanged" must see exactly where it does not.
  *
  * Findings are the things silent elsewhere: a settings file that fails to
@@ -19,19 +19,22 @@
 
 import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
 import { basename, join } from "node:path";
-import { managedSettingsPaths } from "../auto-mode/config.ts";
 import { loadPluginHooks } from "../hooks/plugin-hooks.ts";
 import { type HooksSource, loadHookSettings } from "../hooks/settings.ts";
-import { claudeJsonPath, claudeUserDir } from "../lib/paths.ts";
-import { claudeUserSettingsPath, settingsPaths } from "../lib/claude-settings.ts";
-import { discoverContextFilePaths } from "../lib/claude-context.ts";
-import { CLAUDE_MD_CHAR_LIMIT, claudeMdLimitWarning, indexLimitStatus, projectMemoryDir } from "../lib/memory.ts";
+// Claude Code's auto-memory switch, read through the whole settings ladder.
+import { AUTO_MEMORY_KEY as AUTO_MEMORY } from "../lib/auto-memory.ts";
+import { CONFIG_MODE_KEY, claudeSourcesOn } from "../lib/config-mode.ts";
+import { claudeJsonPath, claudeUserDir, oneCodeStateDir } from "../lib/paths.ts";
+import { claudeUserSettingsPath, managedSettingsPaths, settingsPaths } from "../lib/claude-settings.ts";
+import { discoverContextFilePaths, instructionRule } from "../lib/claude-context.ts";
+import { CLAUDE_MD_CHAR_LIMIT, claudeMdLimitWarning, projectMemoryDir } from "../lib/memory.ts";
+import { indexLimitStatus } from "../lib/memory-content.ts";
 import { readDisabledMcpServers } from "../lib/mcp-overrides.ts";
 import { oneCodeProjectSettingsPath, oneCodeSettingsPath } from "../lib/one-code-settings.ts";
 import { parseFrontmatterLoosely } from "../lib/frontmatter.ts";
 import { defaultDiscoverRoots, discoverPlugins, type DiscoveredPlugins } from "../lib/plugins.ts";
 import { BUNDLED_SKILLS_DIR, promptTemplateNames, scanSkills } from "../lib/skill-scan.ts";
-import { loadServers, type McpServer } from "../mcp/config.ts";
+import { loadServers, type McpServer, piMcpConfigPaths, type RegisteredServer } from "../mcp/config.ts";
 import type { PermissionMode } from "../permissions/matcher.ts";
 import { MODES_NEVER_FROM_PROJECT } from "../permissions/settings.ts";
 import { agentDirs, parseAgentFile } from "../subagents/agents.ts";
@@ -84,14 +87,43 @@ export interface CompatReport {
  * (a checked-in env block must not route subagents).
  */
 const MCP_POLICY_KEYS = ["enableAllProjectMcpServers", "enabledMcpjsonServers", "disabledMcpjsonServers"];
-const CLAUDE_PROJECT_KEYS = new Set(["permissions", "hooks", "enabledPlugins", ...MCP_POLICY_KEYS]);
+/** One Code's workflow keys, read from its user and project files (lib/one-code-settings.ts). */
+const WORKFLOW_KEYS = ["enableWorkflows", "disableWorkflows", "workflowSizeGuideline"];
+const CLAUDE_PROJECT_KEYS = new Set(["permissions", "hooks", "enabledPlugins", AUTO_MEMORY, ...MCP_POLICY_KEYS]);
 const SCOPE_KEYS: Record<SettingsScope, ReadonlySet<string>> = {
-	"claude-user": new Set(["permissions", "hooks", "env", "enabledPlugins", "autoMode", ...MCP_POLICY_KEYS]),
+	"claude-user": new Set(["permissions", "hooks", "env", "enabledPlugins", "autoMode", AUTO_MEMORY, ...MCP_POLICY_KEYS]),
 	"claude-project": CLAUDE_PROJECT_KEYS,
 	"claude-local": CLAUDE_PROJECT_KEYS,
-	managed: new Set(["permissions", "hooks", "env", "autoMode", "enabledPlugins"]),
-	"onecode-user": new Set(["subagentModel", "subagentModelSetFor", "autoMode", "permissions", "webSearch", "disabledMcpServers"]),
-	"onecode-project": new Set(["permissions", "disabledMcpServers"]),
+	managed: new Set(["permissions", "hooks", "env", "autoMode", "enabledPlugins", AUTO_MEMORY]),
+	"onecode-user": new Set([
+		"subagentModel",
+		"subagentModelSetFor",
+		"autoMode",
+		"permissions",
+		"webSearch",
+		"disabledMcpServers",
+		// The /memory panel's two rows (lib/config-mode.ts, lib/auto-memory.ts).
+		CONFIG_MODE_KEY,
+		AUTO_MEMORY,
+		"modelTiers",
+		"suggestNewerModels",
+		"refreshModelCatalog",
+		"artifacts",
+		...WORKFLOW_KEYS,
+		// Remembered "No" answers to startup questions (branding/declined.ts).
+		"compactionKeepDeclined",
+		"piBuiltinsTurnOffDeclined",
+	]),
+	"onecode-project": new Set([
+		"permissions",
+		"disabledMcpServers",
+		AUTO_MEMORY,
+		...WORKFLOW_KEYS,
+		// The external CLAUDE.md includes answer, per repository (lib/claude-external-includes.ts).
+		"hasClaudeMdExternalIncludesApproved",
+		"hasClaudeMdExternalIncludesWarningShown",
+		"claudeMdExternalIncludesRoot",
+	]),
 	"claude-json": new Set(),
 };
 /** Never worth reporting as "ignored". */
@@ -146,7 +178,11 @@ function permissionsSummary(perms: unknown, scope: SettingsScope, findings: Find
 		}
 	}
 	if (p.disableBypassPermissionsMode === "disable") parts.push("bypass mode disabled");
-	if (p.additionalDirectories !== undefined) parts.push("additionalDirectories (not honoured)");
+	if (Array.isArray(p.additionalDirectories) && p.additionalDirectories.length > 0) {
+		const dirs = p.additionalDirectories.length;
+		const fromRepo = scope === "claude-project" || scope === "claude-local";
+		parts.push(`${dirs} workspace director${dirs === 1 ? "y" : "ies"}${fromRepo ? " (applied once you trust the repository's settings)" : ""}`);
+	}
 	return { used: parts.length ? `permissions: ${parts.join("; ")}` : undefined, refused };
 }
 
@@ -208,12 +244,13 @@ function summarizeFile(scope: SettingsScope, label: string, path: string, home:
 		const auto = file.autoMode as Json;
 		const keys = Object.keys(auto);
 		if (known.has("autoMode")) {
+			// `classifierModel` is One Code's own key, read from ~/.onecode only.
 			if (scope === "claude-user" && ("classifierModel" in auto || "classifierModelSetFor" in auto)) {
 				report.refused.push("autoMode.classifierModel — One Code's own key, read from ~/.onecode/settings.json only");
 				findings.push({
 					level: "warn",
-					text: `${shortenHome(path, home)} carries autoMode.classifierModel, a One Code key that is now read only from ~/.onecode/settings.json; the value here is ignored.`,
-					fix: "Move it with /auto-mode model (which writes the new location) and delete the stale key from ~/.claude/settings.json.",
+					text: `${shortenHome(path, home)} carries autoMode.classifierModel, a One Code key read only from ~/.onecode/settings.json; the value here is ignored.`,
+					fix: "Set it with /auto-mode model (which writes ~/.onecode/settings.json) and delete the stale key from ~/.claude/settings.json.",
 				});
 			}
 			const consumed = keys.filter((k) => !(scope === "claude-user" && (k === "classifierModel" || k === "classifierModelSetFor")));
@@ -237,6 +274,7 @@ function summarizeFile(scope: SettingsScope, label: string, path: string, home:
 		});
 	}
 	if (scope === "onecode-user") {
+		if (typeof file.configMode === "string") report.used.push(`configMode "${file.configMode}" (/memory config sources)`);
 		if (typeof file.subagentModel === "string") report.used.push(`subagentModel "${file.subagentModel}"`);
 		if (file.webSearch && typeof file.webSearch === "object") report.used.push("webSearch (keys/order for the search fallback)");
 	}
@@ -244,6 +282,7 @@ function summarizeFile(scope: SettingsScope, label: string, path: string, home:
 		if (key in file && known.has(key)) report.used.push(`${key}: ${Array.isArray(file[key]) ? count(file[key]) : String(file[key])}`);
 	}
 	if ("disabledMcpServers" in file && known.has("disabledMcpServers")) report.used.push(`disabledMcpServers: ${count(file.disabledMcpServers)} (via /mcp disable)`);
+	if (typeof file[AUTO_MEMORY] === "boolean" && known.has(AUTO_MEMORY)) report.used.push(`${AUTO_MEMORY}: ${file[AUTO_MEMORY]}`);
 
 	for (const key of Object.keys(file)) {
 		if (known.has(key) || SILENT_KEYS.has(key) || handled.has(key)) continue;
@@ -279,6 +318,10 @@ export interface CompatInput {
 	env: NodeJS.ProcessEnv;
 	/** `<package>/agents`, so bundled agents are counted. */
 	bundledAgentsDir?: string;
+	/** pi's `CONFIG_DIR_NAME` (`.pi` when absent): where the project's pi `mcp.json` is. */
+	piConfigDirName?: string;
+	/** MCP servers other extensions registered, as the session loads them. */
+	registeredMcpServers?: readonly RegisteredServer[];
 }
 
 export function collectCompat(input: CompatInput): CompatReport {
@@ -287,22 +330,38 @@ export function collectCompat(input: CompatInput): CompatReport {
 	const claudeDir = claudeUserDir(home, env);
 	const claude = settingsPaths(cwd, home);
 
+	// Independent mode (lib/config-mode.ts) reads none of Claude Code's files, so
+	// none is opened here; an organisation's policy file it ignores is named.
+	const independent = !claudeSourcesOn();
 	const files: SettingsFileReport[] = [
-		summarizeFile("claude-user", "Claude Code user settings", claudeUserSettingsPath(home), home, findings),
-		summarizeFile("claude-project", "project settings (checked in)", claude.project, home, findings),
-		summarizeFile("claude-local", "project settings (local)", claude.local, home, findings),
-		...managedSettingsPaths().map((path) => summarizeFile("managed", "managed settings (organisation policy)", path, home, findings)),
-		summarizeFile("claude-json", "Claude Code's .claude.json", claudeJsonPath(home, env), home, findings),
+		...(independent
+			? []
+			: [
+					summarizeFile("claude-user", "Claude Code user settings", claudeUserSettingsPath(home), home, findings),
+					summarizeFile("claude-project", "project settings (checked in)", claude.project, home, findings),
+					summarizeFile("claude-local", "project settings (local)", claude.local, home, findings),
+					...managedSettingsPaths().map((path) => summarizeFile("managed", "managed settings (organisation policy)", path, home, findings)),
+					summarizeFile("claude-json", "Claude Code's .claude.json", claudeJsonPath(home, env), home, findings),
+				]),
 		summarizeFile("onecode-user", "One Code user settings", oneCodeSettingsPath(home, env), home, findings),
 		summarizeFile("onecode-project", "One Code per-repository settings", oneCodeProjectSettingsPath(cwd, home, env), home, findings),
 	];
+	if (independent) {
+		for (const path of managedSettingsPaths().filter((managed) => existsSync(managed))) {
+			findings.push({
+				level: "warn",
+				text: `An organisation policy file exists at ${path}, and independent mode does not apply it.`,
+				fix: "Switch config sources to Claude-compatible in /memory if this machine's policy must hold.",
+			});
+		}
+	}
 
 	// Context files, sized — the block every turn pays for.
 	const contextFiles: ContextFileReport[] = discoverContextFilePaths({
 		cwd,
 		homeClaudeDir: claudeDir,
-		homeOneCodeDir: join(home, ".onecode"),
-		agentsFallback: true,
+		homeOneCodeDir: oneCodeStateDir(env, home),
+		rule: instructionRule(home),
 	}).map(({ path, descriptor }) => {
 		let chars = 0;
 		try {
@@ -401,7 +460,8 @@ export function collectCompat(input: CompatInput): CompatReport {
 	const hookDiagnostics: string[] = [];
 	const hooksLoaded = loadHookSettings(claudeDir, cwd);
 	hookDiagnostics.push(...hooksLoaded.diagnostics);
-	const pluginHooks = discovered ? loadPluginHooks(defaultDiscoverRoots(agentDir, cwd, home), hookDiagnostics) : [];
+	// Runtime dispatch skips plugin hooks when settings disable hooks; report what runs.
+	const pluginHooks = discovered && !hooksLoaded.disabled ? loadPluginHooks(defaultDiscoverRoots(agentDir, cwd, home), hookDiagnostics) : [];
 	const hookSources = [...hooksLoaded.sources, ...pluginHooks];
 	const hookCommands = hookSources.reduce(
 		(n, source) => n + Object.values(source.config).reduce((m, groups) => m + (groups ?? []).reduce((k, g) => k + g.hooks.length, 0), 0),
@@ -411,11 +471,16 @@ export function collectCompat(input: CompatInput): CompatReport {
 
 	// MCP.
 	const configErrors: string[] = [];
+	const configNotes: string[] = [];
 	const servers = loadServers(cwd, home, env, discovered?.mcpConfigs ?? [], {
 		pluginNames: discovered?.mcpConfigPlugins,
 		onError: (path, message) => configErrors.push(`${shortenHome(path, home)}: ${message}`),
+		piConfigs: piMcpConfigPaths(agentDir, cwd, input.piConfigDirName),
+		onNote: (message) => configNotes.push(message),
+		registered: input.registeredMcpServers,
 	});
 	for (const error of configErrors) findings.push({ level: "error", text: `MCP config ${error} — its servers are not loaded.`, fix: "Fix the JSON and run /mcp reconnect." });
+	for (const note of configNotes) findings.push({ level: "warn", text: note });
 	for (const server of servers) {
 		if (server.missingEnv?.length) {
 			findings.push({

package/extensions/doctor/dependencies.ts

@@ -11,13 +11,13 @@
  * providers it depends on a third-party key.
  */
 
-import { existsSync } from "node:fs";
+import { type Dirent, existsSync, readdirSync } from "node:fs";
 import { join } from "node:path";
 import { whichOnPath } from "../lib/which.ts";
 import type { Api, Model } from "@earendil-works/pi-ai";
 import { getProviderKind } from "pi-web-search/src/api.ts";
 import { installHint, serverInstallHint } from "../lsp/install-hints.ts";
-import { SERVERS } from "../lsp/servers.ts";
+import { languageIdForPath, SERVERS } from "../lsp/servers.ts";
 import { typescriptPreflight } from "../lsp/servers.ts";
 import type { McpServer } from "../mcp/config.ts";
 import { BRAVE_KEY_ENV, resolveChain, TAVILY_KEY_ENV, type WebSearchSettings } from "../web/backends.ts";
@@ -44,13 +44,49 @@ export interface DependencyReport {
 	findings: Finding[];
 }
 
-/** Languages the working directory plausibly contains, by the LSP table's own root markers. */
+/** Folders the language scan never enters: dependencies, build output, virtual environments. */
+const SCAN_SKIP = new Set(["node_modules", "vendor", "dist", "build", "out", "target", "venv", "env", "__pycache__", "coverage"]);
+const SCAN_MAX_DEPTH = 4;
+const SCAN_MAX_ENTRIES = 5000;
+
+/**
+ * Languages the working directory contains: by the LSP table's own root
+ * markers, or by a source file the language server would open. The file scan
+ * is bounded (a few levels deep, a few thousand entries, no dot, dependency
+ * or build folders), so a project with `.py` files and no `pyproject.toml`,
+ * or TypeScript under `web/src`, still counts.
+ */
 export function projectLanguages(cwd: string): string[] {
 	const seen = new Map<string, string>(); // command → languageId (one per server binary)
 	for (const [languageId, config] of Object.entries(SERVERS)) {
 		if (seen.has(config.command)) continue;
 		if (config.rootMarkers.some((marker) => existsSync(join(cwd, marker)))) seen.set(config.command, languageId);
 	}
+	// One entry per server binary: the walk stops once every one is accounted for.
+	const servers = new Set(Object.values(SERVERS).map((config) => config.command)).size;
+	if (seen.size < servers) {
+		let visited = 0;
+		const walk = (dir: string, depth: number): void => {
+			let entries: Dirent[];
+			try {
+				entries = readdirSync(dir, { withFileTypes: true });
+			} catch {
+				return;
+			}
+			for (const entry of entries) {
+				if (++visited > SCAN_MAX_ENTRIES || seen.size === servers) return;
+				if (entry.name.startsWith(".")) continue;
+				if (entry.isDirectory()) {
+					if (depth < SCAN_MAX_DEPTH && !SCAN_SKIP.has(entry.name)) walk(join(dir, entry.name), depth + 1);
+					continue;
+				}
+				const languageId = languageIdForPath(entry.name);
+				const config = languageId ? SERVERS[languageId] : undefined;
+				if (languageId && config && !seen.has(config.command)) seen.set(config.command, languageId);
+			}
+		};
+		walk(cwd, 0);
+	}
 	return [...seen.values()];
 }
 
@@ -112,8 +148,8 @@ export function checkDependencies(input: DependencyInput): DependencyReport {
 	const which = (command: string) => whichOnPath(command, env, platform);
 
 	const git = which("git");
-	checks.push({ name: "git", found: !!git, path: git, need: "required", reason: "repository detection, auto mode's recoverability check, worktree isolation", hint: "https://git-scm.com/downloads" });
-	if (!git) findings.push({ level: "warn", text: "git is not on PATH: worktree isolation and auto mode's git-recoverability check are unavailable.", fix: "Install git and make sure it is on the PATH used to launch One Code." });
+	checks.push({ name: "git", found: !!git, path: git, need: "required", reason: "repository detection, auto mode's git status line for the classifier, worktree isolation", hint: "https://git-scm.com/downloads" });
+	if (!git) findings.push({ level: "warn", text: "git is not on PATH: worktree isolation and auto mode's git status line for the classifier are unavailable.", fix: "Install git and make sure it is on the PATH used to launch One Code." });
 
 	// pi downloads ripgrep into <agentDir>/bin on first run when PATH has none
 	// and puts that dir on the shell tools' PATH, so a copy there is "found".

package/extensions/doctor/fix-prompt.ts

@@ -8,7 +8,7 @@
  *
  *   - settings writes go to One Code's OWN files (`~/.onecode/settings.json`,
  *     `~/.onecode/projects/<slug>/settings.json`), never to `~/.claude`, which
- *     One Code treats as read-only (docs/decisions/memory-state.md);
+ *     One Code treats as read-only (working-docs/decisions/memory-state.md);
  *   - session transcripts are pi's JSONL under `<agentDir>/sessions/`, not
  *     Claude Code's `~/.claude/projects/`, and there are no usage counters, so
  *     transcripts are the only usage signal;
@@ -19,7 +19,7 @@
  * Claude Code's ground rules (propose → confirm → apply in at most two
  * questions; key-scoped reads; never inline harvested names into shell
  * commands; transcripts are untrusted data; write for a first-time user) are
- * kept in substance. Rationale: docs/decisions/doctor.md.
+ * kept in substance. Rationale: working-docs/decisions/doctor.md.
  */
 
 import { modeCycleKey } from "../lib/keys.ts";
@@ -38,8 +38,14 @@ export interface FixPromptInput {
 	oneCodeProjectSettingsPath: string;
 	/** True when auto mode is writing `auto-mode-decisions.jsonl` next to the session files. */
 	decisionLogEnabled: boolean;
+	/** True in independent mode (lib/config-mode.ts), where none of Claude Code's files are read. */
+	independent?: boolean;
 }
 
+/** The ground rule that maps the Claude Code paths the prompt names to independent mode's own. */
+const INDEPENDENT_RULE =
+	"- **This session runs in independent mode.** One Code reads none of the Claude Code locations named below (`~/.claude`, `.claude/`, `CLAUDE.md`, `CLAUDE.local.md`, `~/.claude.json`, `.mcp.json`, managed settings). Read each as its One Code counterpart: instructions are `AGENTS.md` and `ONECODE.md`, skills come from `.agents/skills` and pi's skill folders, agents, commands and workflows from `.onecode/` and `~/.onecode/`, settings and hooks from One Code's two settings files, and MCP servers from pi's `mcp.json` files. Propose changes only to those.\n";
+
 export function doctorFixPrompt(input: FixPromptInput): string {
 	const versionCommand =
 		input.install === "app"
@@ -64,6 +70,7 @@ Treat every line of that report as measured fact. Your job on those sections is
 
 ## Ground rules
 
+${input.independent ? INDEPENDENT_RULE : ""}
 - **Propose, then confirm, then apply — and recommend, don't just offer.** Run every check read-only first and present the full report. Then confirm in at most TWO questions with the \`ask_user_question\` tool — never a question per check. (1) ONE consolidated cleanup question covering checks 0-4 and 7: options "Clean up everything (recommended)" first, "Let me pick" second, "No, keep everything" last; only if the user picks "Let me pick", ask one follow-up multi-select with an option per action group (at most 4 options per question — split if there are more groups). (2) A SEPARATE permission question for check 9, never folded into the cleanup bundle: it changes what runs without asking, so it names every allow rule string it would add, and is skipped when nothing was proposed. Put the recommended action FIRST with "(recommended)" in its label and the decline option last. Never edit any file before its group is confirmed.
 - **One Code never writes Claude Code's files.** \`~/.claude/settings.json\`, \`~/.claude.json\`, \`~/.claude/CLAUDE.md\` and the rest of \`~/.claude\` are a read-only compatibility surface here. Settings you change go to One Code's own files: \`${input.oneCodeSettingsPath}\` (user scope) and \`${input.oneCodeProjectSettingsPath}\` (this repository). Skills, plugins and MCP servers are toggled with One Code's commands (\`/skills\`, \`/plugins\`, \`/mcp\`), which persist under One Code's own state, not by editing Claude Code's settings. Only the CLAUDE.md checks (3 and 4) may propose edits to checked-in files, applied as ordinary working-tree edits the user reviews in \`git diff\` — never commit them yourself. \`CLAUDE.local.md\` and the project's own \`.claude/settings.local.json\` are local, uncommitted files and may be edited after confirmation.
 - Token figures are estimates: tokens ≈ characters / 4. Label them "est." everywhere.