apex-code 0.0.1-alpha.1 → 0.0.1-alpha.11

package/dist/core/agent-session-services.js

@@ -1,10 +1,19 @@
 import { join } from "node:path";
-import { getAgentDir } from "../config.js";
+import { getAgentDir, getAuthPath } from "../config.js";
 import { resolvePath } from "../utils/paths.js";
+import { LspDiagnostics } from "./lsp/diagnostics.js";
+import { LspPool } from "./lsp/pool.js";
+import { resolveLspRegistry } from "./lsp/registry.js";
+import { LspStatusStore } from "./lsp/status.js";
 import { ModelRuntime } from "./model-runtime.js";
 import { DefaultResourceLoader, } from "./resource-loader.js";
+import { createSandboxCredentialStore } from "./sandbox/rpc/credential-client.js";
 import { createAgentSession } from "./sdk.js";
 import { SettingsManager } from "./settings-manager.js";
+import { SqliteUsagePerformanceStore } from "./usage-performance-store.js";
+import { createDeferredWebSearchOperations, resolveWebSearchOperations } from "./web-search-provider.js";
+/** Filename of the shared durable-state database within an agent directory (roadmap Phase 8). */
+const DURABLE_STATE_DATABASE_FILENAME = "state.sqlite";
 function applyExtensionFlagValues(resourceLoader, extensionFlagValues) {
     if (!extensionFlagValues) {
         return [];
@@ -53,13 +62,39 @@ function applyExtensionFlagValues(resourceLoader, extensionFlagValues) {
 export async function createAgentSessionServices(options) {
     const cwd = resolvePath(options.cwd);
     const agentDir = options.agentDir ? resolvePath(options.agentDir) : getAgentDir();
+    const diagnostics = [];
+    // A ledger failure must never block session creation or a turn — open it
+    // best-effort and degrade to a diagnostic, never a thrown error.
+    let usagePerformanceStore;
+    if (!options.modelRuntime) {
+        try {
+            usagePerformanceStore = new SqliteUsagePerformanceStore(join(agentDir, DURABLE_STATE_DATABASE_FILENAME), options.sessionId);
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            diagnostics.push({ type: "warning", message: `Usage/cost recording unavailable: ${message}` });
+        }
+    }
+    const settingsManager = options.settingsManager ?? SettingsManager.create(cwd, agentDir);
+    const otlpEndpoint = settingsManager.getObservabilitySettings().otlpEndpoint;
+    const otlpExportConfig = otlpEndpoint
+        ? { endpoint: otlpEndpoint, headers: settingsManager.getObservabilitySettings().otlpHeaders }
+        : undefined;
+    // Inside a sandboxed session the supervisor advertises a credential write channel
+    // (spec: 2026-08-22-supervisor-mediated-credential-writes). Reads are unchanged --
+    // still the read-only projection of the host credential file -- while writes and
+    // deletes travel the supervisor-owned socket instead of failing on the read-only
+    // mount. Outside a sandbox this resolves to undefined and the default store applies.
+    const sandboxCredentialStore = createSandboxCredentialStore();
     const modelRuntime = options.modelRuntime ??
         (await ModelRuntime.create({
-            authPath: join(agentDir, "auth.json"),
+            authPath: process.env.APEX_CODE_AUTH_PATH ?? (options.agentDir ? join(agentDir, "auth.json") : getAuthPath()),
+            credentials: sandboxCredentialStore,
             modelsPath: join(agentDir, "models.json"),
             signal: options.modelRuntimeSignal,
+            usagePerformanceStore,
+            otlpExportConfig,
         }));
-    const settingsManager = options.settingsManager ?? SettingsManager.create(cwd, agentDir);
     const resourceLoader = new DefaultResourceLoader({
         ...(options.resourceLoaderOptions ?? {}),
         cwd,
@@ -67,7 +102,6 @@ export async function createAgentSessionServices(options) {
         settingsManager,
     });
     await resourceLoader.reload(options.resourceLoaderReloadOptions);
-    const diagnostics = [];
     const extensionsResult = resourceLoader.getExtensions();
     for (const { name, config, extensionPath } of extensionsResult.runtime.pendingProviderRegistrations) {
         try {
@@ -97,13 +131,80 @@ export async function createAgentSessionServices(options) {
     extensionsResult.runtime.pendingNativeProviderRegistrations = [];
     await modelRuntime.refresh({ allowNetwork: false });
     diagnostics.push(...applyExtensionFlagValues(resourceLoader, options.extensionFlagValues));
+    // `lspStatus` is constructed unconditionally (and outside the try) so it always
+    // records real state transitions the pool experiences below, including the
+    // eager-start failure the catch block handles -- not just a snapshot taken at one
+    // fixed point in time.
+    const lspStatus = new LspStatusStore();
+    let lspPool;
+    let registry;
+    let lspConfigured = false;
+    try {
+        registry = resolveLspRegistry(settingsManager.getLspSettings(), { workspace: cwd });
+        lspPool = new LspPool(registry, {
+            onStatusChange: (status) => lspStatus.record({
+                serverId: status.serverId,
+                root: status.root,
+                state: status.state,
+                attempt: status.attempts,
+                ...(status.reason === undefined ? {} : { reason: status.reason }),
+            }),
+        });
+        lspConfigured = registry.servers.length > 0;
+        // Per the spec's "Resolved configuration, ownership, and lifecycle": any
+        // configured entry that cannot resolve, spawn, or initialize its cwd-root
+        // process within its timeout is a startup misconfiguration -- fail fast here,
+        // following core/permissions/startup.ts's precedent, rather than let a broken
+        // server surface only when a tool call needs it mid-run.
+        if (lspConfigured)
+            await lspPool.start();
+    }
+    catch (error) {
+        // Name the failing binary(ies), not just the raw client/registry error: the
+        // registry itself already does this for a resolution failure (missing/
+        // un-spawnable binary names the command and lookup path), but a `pool.start()`
+        // rejection surfaces only the first client's bare error (e.g. "initialize timed
+        // out"), with no server id attached. `registry.servers` (resolved commands) and
+        // `lspPool.status()` (which entries actually failed) are both in scope here, so
+        // build the richer message without changing `LspPoolStatus`'s shape or the
+        // pool's own error-propagation wire format.
+        const commandById = new Map(registry?.servers.map((server) => [server.id, server.command]) ?? []);
+        const failedEntries = (lspPool?.status() ?? []).filter((status) => status.state === "degraded" || status.state === "disabled");
+        const message = failedEntries.length > 0
+            ? failedEntries
+                .map((status) => `${status.serverId} (${commandById.get(status.serverId) ?? "?"}) at ${status.root}: ${status.reason ?? "unknown error"}`)
+                .join("; ")
+            : error instanceof Error
+                ? error.message
+                : String(error);
+        diagnostics.push({ type: "error", message: `LSP startup failed: ${message}` });
+        // A pool that got partway through eager start may already have spawned and
+        // initialized sibling servers successfully; discarding it without disposing
+        // would orphan those child processes rather than tearing them down cleanly.
+        await lspPool?.dispose().catch(() => { });
+        lspConfigured = false;
+        lspPool = new LspPool({ workspace: cwd, servers: [], platform: process.platform });
+    }
+    const lspDiagnostics = new LspDiagnostics(lspPool);
     return {
         cwd,
         agentDir,
         modelRuntime,
         settingsManager,
         resourceLoader,
+        lspPool,
+        lspDiagnostics,
+        lspConfigured,
+        lspStatus,
         diagnostics,
+        close: async () => {
+            // Diagnostics first: it still needs live LSP clients to send didClose
+            // during its own teardown, so it must not outlive the pool it wraps.
+            await lspDiagnostics.dispose();
+            await lspPool.dispose();
+            if (!options.modelRuntime)
+                modelRuntime.close();
+        },
     };
 }
 /**
@@ -114,6 +215,37 @@ export async function createAgentSessionServices(options) {
  * cwd before constructing the session.
  */
 export async function createAgentSessionFromServices(options) {
+    const { lspPool, lspDiagnostics, lspConfigured } = options.services;
+    // Both gated on `lspConfigured` (at least one server resolved), not per-path:
+    // the spec's "no diagnostics injection or result change whatsoever when `lsp` is
+    // unconfigured" is a session-level guarantee. A session with servers configured
+    // for *some* languages still injects diagnosticsOperations -- a mutated path with
+    // no matching server correctly resolves to the explicit `unavailable` outcome via
+    // `LspDiagnostics.afterMutation`'s own per-path `pool.acquire`, it is simply never
+    // asked at all when the session has no servers whatsoever. `lspDiagnostics`
+    // already matches `DiagnosticsOperations` structurally, so it is passed directly
+    // rather than wrapped.
+    const diagnosticsOperations = lspConfigured ? lspDiagnostics : undefined;
+    const lspOperations = lspConfigured
+        ? {
+            request: async (absolutePath, method, params, signal) => {
+                const connection = await lspPool.acquire(absolutePath);
+                if (!connection)
+                    return undefined;
+                return connection.client.request(method, params, signal);
+            },
+        }
+        : undefined;
+    // Read per call rather than captured here. The tool registry is built once at
+    // session construction, so a key saved from the settings panel mid-session would
+    // otherwise not take effect until restart.
+    // Two different questions. Whether a credential resolves *now* decides whether the
+    // tool is active, because activation happens once at construction. Resolution then
+    // stays deferred so a key changed mid-session is picked up without a restart.
+    const settingsManager = options.services.settingsManager;
+    const webSearchOperations = resolveWebSearchOperations(settingsManager.getWebSearchSettings())
+        ? createDeferredWebSearchOperations(() => settingsManager.getWebSearchSettings())
+        : undefined;
     return createAgentSession({
         cwd: options.services.cwd,
         agentDir: options.services.agentDir,
@@ -129,6 +261,10 @@ export async function createAgentSessionFromServices(options) {
         noTools: options.noTools,
         customTools: options.customTools,
         sessionStartEvent: options.sessionStartEvent,
+        permissionGate: options.permissionGate,
+        diagnosticsOperations,
+        lspOperations,
+        webSearchOperations,
     });
 }
 //# sourceMappingURL=agent-session-services.js.map

package/dist/core/agent-session-services.js.map

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{ join } from \"node:path\";\nimport type { Model } from \"@earendil-works/pi-ai\";\nimport type { ThinkingLevel } from \"apex-code-agent-core\";\nimport { getAgentDir } from \"../config.ts\";\nimport { resolvePath } from \"../utils/paths.ts\";\nimport type { SessionStartEvent, ToolDefinition } from \"./extensions/index.ts\";\nimport { ModelRuntime } from \"./model-runtime.ts\";\nimport {\n\tDefaultResourceLoader,\n\ttype DefaultResourceLoaderOptions,\n\ttype ResourceLoader,\n\ttype ResourceLoaderReloadOptions,\n} from \"./resource-loader.ts\";\nimport { type CreateAgentSessionOptions, type CreateAgentSessionResult, createAgentSession } from \"./sdk.ts\";\nimport type { SessionManager } from \"./session-manager.ts\";\nimport { SettingsManager } from \"./settings-manager.ts\";\n\n/**\n * Non-fatal issues collected while creating services or sessions.\n *\n * Runtime creation returns diagnostics to the caller instead of printing or\n * exiting. The app layer decides whether warnings should be shown and whether\n * errors should abort startup.\n */\nexport interface AgentSessionRuntimeDiagnostic {\n\ttype: \"info\" | \"warning\" | \"error\";\n\tmessage: string;\n}\n\n/**\n * Inputs for creating cwd-bound runtime services.\n *\n * These services are recreated whenever the effective session cwd changes.\n * CLI-provided resource paths should be resolved to absolute paths before they\n * reach this function, so later cwd switches do not reinterpret them.\n */\nexport interface CreateAgentSessionServicesOptions {\n\tcwd: string;\n\tagentDir?: string;\n\tsettingsManager?: SettingsManager;\n\tmodelRuntime?: ModelRuntime;\n\tmodelRuntimeSignal?: AbortSignal;\n\textensionFlagValues?: Map<string, boolean | string>;\n\tresourceLoaderOptions?: Omit<DefaultResourceLoaderOptions, \"cwd\" | \"agentDir\" | \"settingsManager\">;\n\tresourceLoaderReloadOptions?: ResourceLoaderReloadOptions;\n}\n\n/**\n * Inputs for creating an AgentSession from already-created services.\n *\n * Use this after services exist and any cwd-bound model/tool/session options\n * have been resolved against those services.\n */\nexport interface CreateAgentSessionFromServicesOptions {\n\tservices: AgentSessionServices;\n\tsessionManager: SessionManager;\n\tsessionStartEvent?: SessionStartEvent;\n\tmodel?: Model<any>;\n\tthinkingLevel?: ThinkingLevel;\n\tscopedModels?: Array<{ model: Model<any>; thinkingLevel?: ThinkingLevel }>;\n\ttools?: string[];\n\texcludeTools?: CreateAgentSessionOptions[\"excludeTools\"];\n\tnoTools?: CreateAgentSessionOptions[\"noTools\"];\n\tcustomTools?: ToolDefinition[];\n}\n\n/**\n * Coherent cwd-bound runtime services for one effective session cwd.\n *\n * This is infrastructure only. The AgentSession itself is created separately so\n * session options can be resolved against these services first.\n */\nexport interface AgentSessionServices {\n\tcwd: string;\n\tagentDir: string;\n\tmodelRuntime: ModelRuntime;\n\tsettingsManager: SettingsManager;\n\tresourceLoader: ResourceLoader;\n\tdiagnostics: AgentSessionRuntimeDiagnostic[];\n}\n\nfunction applyExtensionFlagValues(\n\tresourceLoader: ResourceLoader,\n\textensionFlagValues: Map<string, boolean | string> | undefined,\n): AgentSessionRuntimeDiagnostic[] {\n\tif (!extensionFlagValues) {\n\t\treturn [];\n\t}\n\n\tconst diagnostics: AgentSessionRuntimeDiagnostic[] = [];\n\tconst extensionsResult = resourceLoader.getExtensions();\n\tconst registeredFlags = new Map<string, { type: \"boolean\" | \"string\" }>();\n\tfor (const extension of extensionsResult.extensions) {\n\t\tfor (const [name, flag] of extension.flags) {\n\t\t\tregisteredFlags.set(name, { type: flag.type });\n\t\t}\n\t}\n\n\tconst unknownFlags: string[] = [];\n\tfor (const [name, value] of extensionFlagValues) {\n\t\tconst flag = registeredFlags.get(name);\n\t\tif (!flag) {\n\t\t\tunknownFlags.push(name);\n\t\t\tcontinue;\n\t\t}\n\t\tif (flag.type === \"boolean\") {\n\t\t\textensionsResult.runtime.flagValues.set(name, true);\n\t\t\tcontinue;\n\t\t}\n\t\tif (typeof value === \"string\") {\n\t\t\textensionsResult.runtime.flagValues.set(name, value);\n\t\t\tcontinue;\n\t\t}\n\t\tdiagnostics.push({\n\t\t\ttype: \"error\",\n\t\t\tmessage: `Extension flag \"--${name}\" requires a value`,\n\t\t});\n\t}\n\n\tif (unknownFlags.length > 0) {\n\t\tdiagnostics.push({\n\t\t\ttype: \"error\",\n\t\t\tmessage: `Unknown option${unknownFlags.length === 1 ? \"\" : \"s\"}: ${unknownFlags.map((name) => `--${name}`).join(\", \")}`,\n\t\t});\n\t}\n\n\treturn diagnostics;\n}\n\n/**\n * Create cwd-bound runtime services.\n *\n * Returns services plus diagnostics. It does not create an AgentSession.\n */\nexport async function createAgentSessionServices(\n\toptions: CreateAgentSessionServicesOptions,\n): Promise<AgentSessionServices> {\n\tconst cwd = resolvePath(options.cwd);\n\tconst agentDir = options.agentDir ? resolvePath(options.agentDir) : getAgentDir();\n\tconst modelRuntime =\n\t\toptions.modelRuntime ??\n\t\t(await ModelRuntime.create({\n\t\t\tauthPath: join(agentDir, \"auth.json\"),\n\t\t\tmodelsPath: join(agentDir, \"models.json\"),\n\t\t\tsignal: options.modelRuntimeSignal,\n\t\t}));\n\tconst settingsManager = options.settingsManager ?? SettingsManager.create(cwd, agentDir);\n\tconst resourceLoader = new DefaultResourceLoader({\n\t\t...(options.resourceLoaderOptions ?? {}),\n\t\tcwd,\n\t\tagentDir,\n\t\tsettingsManager,\n\t});\n\tawait resourceLoader.reload(options.resourceLoaderReloadOptions);\n\n\tconst diagnostics: AgentSessionRuntimeDiagnostic[] = [];\n\tconst extensionsResult = resourceLoader.getExtensions();\n\tfor (const { name, config, extensionPath } of extensionsResult.runtime.pendingProviderRegistrations) {\n\t\ttry {\n\t\t\tmodelRuntime.registerProvider(name, config);\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : String(error);\n\t\t\tdiagnostics.push({\n\t\t\t\ttype: \"error\",\n\t\t\t\tmessage: `Extension \"${extensionPath}\" error: ${message}`,\n\t\t\t});\n\t\t}\n\t}\n\textensionsResult.runtime.pendingProviderRegistrations = [];\n\tfor (const { provider, extensionPath } of extensionsResult.runtime.pendingNativeProviderRegistrations) {\n\t\ttry {\n\t\t\tmodelRuntime.registerNativeProvider(provider);\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : String(error);\n\t\t\tdiagnostics.push({\n\t\t\t\ttype: \"error\",\n\t\t\t\tmessage: `Extension \"${extensionPath}\" error: ${message}`,\n\t\t\t});\n\t\t}\n\t}\n\textensionsResult.runtime.pendingNativeProviderRegistrations = [];\n\tawait modelRuntime.refresh({ allowNetwork: false });\n\tdiagnostics.push(...applyExtensionFlagValues(resourceLoader, options.extensionFlagValues));\n\n\treturn {\n\t\tcwd,\n\t\tagentDir,\n\t\tmodelRuntime,\n\t\tsettingsManager,\n\t\tresourceLoader,\n\t\tdiagnostics,\n\t};\n}\n\n/**\n * Create an AgentSession from previously created services.\n *\n * This keeps session creation separate from service creation so callers can\n * resolve model, thinking, tools, and other session inputs against the target\n * cwd before constructing the session.\n */\nexport async function createAgentSessionFromServices(\n\toptions: CreateAgentSessionFromServicesOptions,\n): Promise<CreateAgentSessionResult> {\n\treturn createAgentSession({\n\t\tcwd: options.services.cwd,\n\t\tagentDir: options.services.agentDir,\n\t\tmodelRuntime: options.services.modelRuntime,\n\t\tsettingsManager: options.services.settingsManager,\n\t\tresourceLoader: options.services.resourceLoader,\n\t\tsessionManager: options.sessionManager,\n\t\tmodel: options.model,\n\t\tthinkingLevel: options.thinkingLevel,\n\t\tscopedModels: options.scopedModels,\n\t\ttools: options.tools,\n\t\texcludeTools: options.excludeTools,\n\t\tnoTools: options.noTools,\n\t\tcustomTools: options.customTools,\n\t\tsessionStartEvent: options.sessionStartEvent,\n\t});\n}\n"]}
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{ join } from \"node:path\";\nimport type { Model } from \"@earendil-works/pi-ai\";\nimport type { ThinkingLevel } from \"apex-code-agent-core\";\nimport { getAgentDir, getAuthPath } from \"../config.ts\";\nimport { resolvePath } from \"../utils/paths.ts\";\nimport type { SessionStartEvent, ToolDefinition } from \"./extensions/index.ts\";\nimport { LspDiagnostics } from \"./lsp/diagnostics.ts\";\nimport { LspPool } from \"./lsp/pool.ts\";\nimport { resolveLspRegistry } from \"./lsp/registry.ts\";\nimport { LspStatusStore } from \"./lsp/status.ts\";\nimport { ModelRuntime } from \"./model-runtime.ts\";\nimport type { PermissionGateOptions } from \"./permissions/gate.ts\";\nimport {\n\tDefaultResourceLoader,\n\ttype DefaultResourceLoaderOptions,\n\ttype ResourceLoader,\n\ttype ResourceLoaderReloadOptions,\n} from \"./resource-loader.ts\";\nimport { createSandboxCredentialStore } from \"./sandbox/rpc/credential-client.ts\";\nimport { type CreateAgentSessionOptions, type CreateAgentSessionResult, createAgentSession } from \"./sdk.ts\";\nimport type { SessionManager } from \"./session-manager.ts\";\nimport { SettingsManager } from \"./settings-manager.ts\";\nimport type { LspOperations } from \"./tools/lsp.ts\";\nimport { SqliteUsagePerformanceStore } from \"./usage-performance-store.ts\";\nimport { createDeferredWebSearchOperations, resolveWebSearchOperations } from \"./web-search-provider.ts\";\n\n/** Filename of the shared durable-state database within an agent directory (roadmap Phase 8). */\nconst DURABLE_STATE_DATABASE_FILENAME = \"state.sqlite\";\n\n/**\n * Non-fatal issues collected while creating services or sessions.\n *\n * Runtime creation returns diagnostics to the caller instead of printing or\n * exiting. The app layer decides whether warnings should be shown and whether\n * errors should abort startup.\n */\nexport interface AgentSessionRuntimeDiagnostic {\n\ttype: \"info\" | \"warning\" | \"error\";\n\tmessage: string;\n}\n\n/**\n * Inputs for creating cwd-bound runtime services.\n *\n * These services are recreated whenever the effective session cwd changes.\n * CLI-provided resource paths should be resolved to absolute paths before they\n * reach this function, so later cwd switches do not reinterpret them.\n */\nexport interface CreateAgentSessionServicesOptions {\n\tcwd: string;\n\tagentDir?: string;\n\t/**\n\t * Session id to stamp on every usage-performance sample this runtime records.\n\t * Only observed when `modelRuntime` is not already provided — a caller-supplied\n\t * runtime owns its own store, if any.\n\t */\n\tsessionId?: string;\n\tsettingsManager?: SettingsManager;\n\tmodelRuntime?: ModelRuntime;\n\tmodelRuntimeSignal?: AbortSignal;\n\textensionFlagValues?: Map<string, boolean | string>;\n\tresourceLoaderOptions?: Omit<DefaultResourceLoaderOptions, \"cwd\" | \"agentDir\" | \"settingsManager\">;\n\tresourceLoaderReloadOptions?: ResourceLoaderReloadOptions;\n}\n\n/**\n * Inputs for creating an AgentSession from already-created services.\n *\n * Use this after services exist and any cwd-bound model/tool/session options\n * have been resolved against those services.\n */\nexport interface CreateAgentSessionFromServicesOptions {\n\tservices: AgentSessionServices;\n\tsessionManager: SessionManager;\n\tsessionStartEvent?: SessionStartEvent;\n\tmodel?: Model<any>;\n\tthinkingLevel?: ThinkingLevel;\n\tscopedModels?: Array<{ model: Model<any>; thinkingLevel?: ThinkingLevel }>;\n\ttools?: string[];\n\texcludeTools?: CreateAgentSessionOptions[\"excludeTools\"];\n\tnoTools?: CreateAgentSessionOptions[\"noTools\"];\n\tcustomTools?: ToolDefinition[];\n\tpermissionGate?: Omit<PermissionGateOptions, \"getContract\">;\n}\n\n/**\n * Coherent cwd-bound runtime services for one effective session cwd.\n *\n * This is infrastructure only. The AgentSession itself is created separately so\n * session options can be resolved against these services first.\n */\nexport interface AgentSessionServices {\n\tcwd: string;\n\tagentDir: string;\n\tmodelRuntime: ModelRuntime;\n\tsettingsManager: SettingsManager;\n\tresourceLoader: ResourceLoader;\n\tlspPool: LspPool;\n\t/**\n\t * Wraps `lspPool` for `DiagnosticsOperations.afterMutation` (LSP.4). Structurally\n\t * compatible with `core/tools/diagnostics.ts`'s `DiagnosticsOperations` -- callers\n\t * pass this value directly, never importing `core/lsp/*` themselves.\n\t */\n\tlspDiagnostics: LspDiagnostics;\n\t/** True when at least one LSP server resolved -- gates registering the `lsp` tool (LSP.5). */\n\tlspConfigured: boolean;\n\t/**\n\t * Chronological, bounded record of every server-root state transition observed by\n\t * `lspPool` for this services lifetime (LSP.2). Inspectable structured state -- not\n\t * wired to any user-facing surface by this plan (see `docs/plans/2026-08-18-lsp.md`,\n\t * Task LSP.2: this is not a `/doctor` task).\n\t */\n\tlspStatus: LspStatusStore;\n\tdiagnostics: AgentSessionRuntimeDiagnostic[];\n\tclose(): Promise<void>;\n}\n\nfunction applyExtensionFlagValues(\n\tresourceLoader: ResourceLoader,\n\textensionFlagValues: Map<string, boolean | string> | undefined,\n): AgentSessionRuntimeDiagnostic[] {\n\tif (!extensionFlagValues) {\n\t\treturn [];\n\t}\n\n\tconst diagnostics: AgentSessionRuntimeDiagnostic[] = [];\n\tconst extensionsResult = resourceLoader.getExtensions();\n\tconst registeredFlags = new Map<string, { type: \"boolean\" | \"string\" }>();\n\tfor (const extension of extensionsResult.extensions) {\n\t\tfor (const [name, flag] of extension.flags) {\n\t\t\tregisteredFlags.set(name, { type: flag.type });\n\t\t}\n\t}\n\n\tconst unknownFlags: string[] = [];\n\tfor (const [name, value] of extensionFlagValues) {\n\t\tconst flag = registeredFlags.get(name);\n\t\tif (!flag) {\n\t\t\tunknownFlags.push(name);\n\t\t\tcontinue;\n\t\t}\n\t\tif (flag.type === \"boolean\") {\n\t\t\textensionsResult.runtime.flagValues.set(name, true);\n\t\t\tcontinue;\n\t\t}\n\t\tif (typeof value === \"string\") {\n\t\t\textensionsResult.runtime.flagValues.set(name, value);\n\t\t\tcontinue;\n\t\t}\n\t\tdiagnostics.push({\n\t\t\ttype: \"error\",\n\t\t\tmessage: `Extension flag \"--${name}\" requires a value`,\n\t\t});\n\t}\n\n\tif (unknownFlags.length > 0) {\n\t\tdiagnostics.push({\n\t\t\ttype: \"error\",\n\t\t\tmessage: `Unknown option${unknownFlags.length === 1 ? \"\" : \"s\"}: ${unknownFlags.map((name) => `--${name}`).join(\", \")}`,\n\t\t});\n\t}\n\n\treturn diagnostics;\n}\n\n/**\n * Create cwd-bound runtime services.\n *\n * Returns services plus diagnostics. It does not create an AgentSession.\n */\nexport async function createAgentSessionServices(\n\toptions: CreateAgentSessionServicesOptions,\n): Promise<AgentSessionServices> {\n\tconst cwd = resolvePath(options.cwd);\n\tconst agentDir = options.agentDir ? resolvePath(options.agentDir) : getAgentDir();\n\tconst diagnostics: AgentSessionRuntimeDiagnostic[] = [];\n\n\t// A ledger failure must never block session creation or a turn — open it\n\t// best-effort and degrade to a diagnostic, never a thrown error.\n\tlet usagePerformanceStore: SqliteUsagePerformanceStore | undefined;\n\tif (!options.modelRuntime) {\n\t\ttry {\n\t\t\tusagePerformanceStore = new SqliteUsagePerformanceStore(\n\t\t\t\tjoin(agentDir, DURABLE_STATE_DATABASE_FILENAME),\n\t\t\t\toptions.sessionId,\n\t\t\t);\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : String(error);\n\t\t\tdiagnostics.push({ type: \"warning\", message: `Usage/cost recording unavailable: ${message}` });\n\t\t}\n\t}\n\n\tconst settingsManager = options.settingsManager ?? SettingsManager.create(cwd, agentDir);\n\tconst otlpEndpoint = settingsManager.getObservabilitySettings().otlpEndpoint;\n\tconst otlpExportConfig = otlpEndpoint\n\t\t? { endpoint: otlpEndpoint, headers: settingsManager.getObservabilitySettings().otlpHeaders }\n\t\t: undefined;\n\n\t// Inside a sandboxed session the supervisor advertises a credential write channel\n\t// (spec: 2026-08-22-supervisor-mediated-credential-writes). Reads are unchanged --\n\t// still the read-only projection of the host credential file -- while writes and\n\t// deletes travel the supervisor-owned socket instead of failing on the read-only\n\t// mount. Outside a sandbox this resolves to undefined and the default store applies.\n\tconst sandboxCredentialStore = createSandboxCredentialStore();\n\tconst modelRuntime =\n\t\toptions.modelRuntime ??\n\t\t(await ModelRuntime.create({\n\t\t\tauthPath: process.env.APEX_CODE_AUTH_PATH ?? (options.agentDir ? join(agentDir, \"auth.json\") : getAuthPath()),\n\t\t\tcredentials: sandboxCredentialStore,\n\t\t\tmodelsPath: join(agentDir, \"models.json\"),\n\t\t\tsignal: options.modelRuntimeSignal,\n\t\t\tusagePerformanceStore,\n\t\t\totlpExportConfig,\n\t\t}));\n\tconst resourceLoader = new DefaultResourceLoader({\n\t\t...(options.resourceLoaderOptions ?? {}),\n\t\tcwd,\n\t\tagentDir,\n\t\tsettingsManager,\n\t});\n\tawait resourceLoader.reload(options.resourceLoaderReloadOptions);\n\n\tconst extensionsResult = resourceLoader.getExtensions();\n\tfor (const { name, config, extensionPath } of extensionsResult.runtime.pendingProviderRegistrations) {\n\t\ttry {\n\t\t\tmodelRuntime.registerProvider(name, config);\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : String(error);\n\t\t\tdiagnostics.push({\n\t\t\t\ttype: \"error\",\n\t\t\t\tmessage: `Extension \"${extensionPath}\" error: ${message}`,\n\t\t\t});\n\t\t}\n\t}\n\textensionsResult.runtime.pendingProviderRegistrations = [];\n\tfor (const { provider, extensionPath } of extensionsResult.runtime.pendingNativeProviderRegistrations) {\n\t\ttry {\n\t\t\tmodelRuntime.registerNativeProvider(provider);\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : String(error);\n\t\t\tdiagnostics.push({\n\t\t\t\ttype: \"error\",\n\t\t\t\tmessage: `Extension \"${extensionPath}\" error: ${message}`,\n\t\t\t});\n\t\t}\n\t}\n\textensionsResult.runtime.pendingNativeProviderRegistrations = [];\n\tawait modelRuntime.refresh({ allowNetwork: false });\n\tdiagnostics.push(...applyExtensionFlagValues(resourceLoader, options.extensionFlagValues));\n\n\t// `lspStatus` is constructed unconditionally (and outside the try) so it always\n\t// records real state transitions the pool experiences below, including the\n\t// eager-start failure the catch block handles -- not just a snapshot taken at one\n\t// fixed point in time.\n\tconst lspStatus = new LspStatusStore();\n\tlet lspPool: LspPool | undefined;\n\tlet registry: ReturnType<typeof resolveLspRegistry> | undefined;\n\tlet lspConfigured = false;\n\ttry {\n\t\tregistry = resolveLspRegistry(settingsManager.getLspSettings(), { workspace: cwd });\n\t\tlspPool = new LspPool(registry, {\n\t\t\tonStatusChange: (status) =>\n\t\t\t\tlspStatus.record({\n\t\t\t\t\tserverId: status.serverId,\n\t\t\t\t\troot: status.root,\n\t\t\t\t\tstate: status.state,\n\t\t\t\t\tattempt: status.attempts,\n\t\t\t\t\t...(status.reason === undefined ? {} : { reason: status.reason }),\n\t\t\t\t}),\n\t\t});\n\t\tlspConfigured = registry.servers.length > 0;\n\t\t// Per the spec's \"Resolved configuration, ownership, and lifecycle\": any\n\t\t// configured entry that cannot resolve, spawn, or initialize its cwd-root\n\t\t// process within its timeout is a startup misconfiguration -- fail fast here,\n\t\t// following core/permissions/startup.ts's precedent, rather than let a broken\n\t\t// server surface only when a tool call needs it mid-run.\n\t\tif (lspConfigured) await lspPool.start();\n\t} catch (error) {\n\t\t// Name the failing binary(ies), not just the raw client/registry error: the\n\t\t// registry itself already does this for a resolution failure (missing/\n\t\t// un-spawnable binary names the command and lookup path), but a `pool.start()`\n\t\t// rejection surfaces only the first client's bare error (e.g. \"initialize timed\n\t\t// out\"), with no server id attached. `registry.servers` (resolved commands) and\n\t\t// `lspPool.status()` (which entries actually failed) are both in scope here, so\n\t\t// build the richer message without changing `LspPoolStatus`'s shape or the\n\t\t// pool's own error-propagation wire format.\n\t\tconst commandById = new Map(registry?.servers.map((server) => [server.id, server.command]) ?? []);\n\t\tconst failedEntries = (lspPool?.status() ?? []).filter(\n\t\t\t(status) => status.state === \"degraded\" || status.state === \"disabled\",\n\t\t);\n\t\tconst message =\n\t\t\tfailedEntries.length > 0\n\t\t\t\t? failedEntries\n\t\t\t\t\t\t.map(\n\t\t\t\t\t\t\t(status) =>\n\t\t\t\t\t\t\t\t`${status.serverId} (${commandById.get(status.serverId) ?? \"?\"}) at ${status.root}: ${status.reason ?? \"unknown error\"}`,\n\t\t\t\t\t\t)\n\t\t\t\t\t\t.join(\"; \")\n\t\t\t\t: error instanceof Error\n\t\t\t\t\t? error.message\n\t\t\t\t\t: String(error);\n\t\tdiagnostics.push({ type: \"error\", message: `LSP startup failed: ${message}` });\n\t\t// A pool that got partway through eager start may already have spawned and\n\t\t// initialized sibling servers successfully; discarding it without disposing\n\t\t// would orphan those child processes rather than tearing them down cleanly.\n\t\tawait lspPool?.dispose().catch(() => {});\n\t\tlspConfigured = false;\n\t\tlspPool = new LspPool({ workspace: cwd, servers: [], platform: process.platform });\n\t}\n\tconst lspDiagnostics = new LspDiagnostics(lspPool);\n\n\treturn {\n\t\tcwd,\n\t\tagentDir,\n\t\tmodelRuntime,\n\t\tsettingsManager,\n\t\tresourceLoader,\n\t\tlspPool,\n\t\tlspDiagnostics,\n\t\tlspConfigured,\n\t\tlspStatus,\n\t\tdiagnostics,\n\t\tclose: async () => {\n\t\t\t// Diagnostics first: it still needs live LSP clients to send didClose\n\t\t\t// during its own teardown, so it must not outlive the pool it wraps.\n\t\t\tawait lspDiagnostics.dispose();\n\t\t\tawait lspPool.dispose();\n\t\t\tif (!options.modelRuntime) modelRuntime.close();\n\t\t},\n\t};\n}\n\n/**\n * Create an AgentSession from previously created services.\n *\n * This keeps session creation separate from service creation so callers can\n * resolve model, thinking, tools, and other session inputs against the target\n * cwd before constructing the session.\n */\nexport async function createAgentSessionFromServices(\n\toptions: CreateAgentSessionFromServicesOptions,\n): Promise<CreateAgentSessionResult> {\n\tconst { lspPool, lspDiagnostics, lspConfigured } = options.services;\n\t// Both gated on `lspConfigured` (at least one server resolved), not per-path:\n\t// the spec's \"no diagnostics injection or result change whatsoever when `lsp` is\n\t// unconfigured\" is a session-level guarantee. A session with servers configured\n\t// for *some* languages still injects diagnosticsOperations -- a mutated path with\n\t// no matching server correctly resolves to the explicit `unavailable` outcome via\n\t// `LspDiagnostics.afterMutation`'s own per-path `pool.acquire`, it is simply never\n\t// asked at all when the session has no servers whatsoever. `lspDiagnostics`\n\t// already matches `DiagnosticsOperations` structurally, so it is passed directly\n\t// rather than wrapped.\n\tconst diagnosticsOperations = lspConfigured ? lspDiagnostics : undefined;\n\tconst lspOperations: LspOperations | undefined = lspConfigured\n\t\t? {\n\t\t\t\trequest: async (absolutePath, method, params, signal) => {\n\t\t\t\t\tconst connection = await lspPool.acquire(absolutePath);\n\t\t\t\t\tif (!connection) return undefined;\n\t\t\t\t\treturn connection.client.request(method, params, signal);\n\t\t\t\t},\n\t\t\t}\n\t\t: undefined;\n\n\t// Read per call rather than captured here. The tool registry is built once at\n\t// session construction, so a key saved from the settings panel mid-session would\n\t// otherwise not take effect until restart.\n\t// Two different questions. Whether a credential resolves *now* decides whether the\n\t// tool is active, because activation happens once at construction. Resolution then\n\t// stays deferred so a key changed mid-session is picked up without a restart.\n\tconst settingsManager = options.services.settingsManager;\n\tconst webSearchOperations = resolveWebSearchOperations(settingsManager.getWebSearchSettings())\n\t\t? createDeferredWebSearchOperations(() => settingsManager.getWebSearchSettings())\n\t\t: undefined;\n\n\treturn createAgentSession({\n\t\tcwd: options.services.cwd,\n\t\tagentDir: options.services.agentDir,\n\t\tmodelRuntime: options.services.modelRuntime,\n\t\tsettingsManager: options.services.settingsManager,\n\t\tresourceLoader: options.services.resourceLoader,\n\t\tsessionManager: options.sessionManager,\n\t\tmodel: options.model,\n\t\tthinkingLevel: options.thinkingLevel,\n\t\tscopedModels: options.scopedModels,\n\t\ttools: options.tools,\n\t\texcludeTools: options.excludeTools,\n\t\tnoTools: options.noTools,\n\t\tcustomTools: options.customTools,\n\t\tsessionStartEvent: options.sessionStartEvent,\n\t\tpermissionGate: options.permissionGate,\n\t\tdiagnosticsOperations,\n\t\tlspOperations,\n\t\twebSearchOperations,\n\t});\n}\n"]}

package/dist/core/agent-session.d.ts

@@ -15,15 +15,26 @@
 import type { ImageContent, Model, TextContent } from "@earendil-works/pi-ai/compat";
 import type { Agent, AgentEvent, AgentMessage, AgentState, AgentTool, ThinkingLevel } from "apex-code-agent-core";
 import { type BashResult } from "./bash-executor.ts";
+import type { CheckpointSettings } from "./checkpoints/git-checkpoints.ts";
+import { type SessionCheckpoints } from "./checkpoints/session-checkpoints.ts";
 import { type CompactionResult } from "./compaction/index.ts";
 import { type ContextUsage, type ExtensionCommandContextActions, type ExtensionErrorListener, type ExtensionMode, ExtensionRunner, type ExtensionUIContext, type InputSource, type ReplacedSessionContext, type SessionStartEvent, type ShutdownHandler, type ToolDefinition, type ToolInfo } from "./extensions/index.ts";
+import type { McpRuntime } from "./mcp/runtime.ts";
 import type { CustomMessage } from "./messages.ts";
 import type { ModelRuntime } from "./model-runtime.ts";
+import { type PermissionGateOptions } from "./permissions/gate.ts";
+import { type EffectiveModeResolution } from "./permissions/startup.ts";
+import type { PermissionMode } from "./permissions/store.ts";
 import { type PromptTemplate } from "./prompt-templates.ts";
 import type { ResourceLoader } from "./resource-loader.ts";
 import type { BranchSummaryEntry, SessionEntry, SessionManager } from "./session-manager.ts";
 import type { SettingsManager } from "./settings-manager.ts";
 import { type BashOperations } from "./tools/bash.ts";
+import type { EvidenceSink } from "./tools/contract.ts";
+import { type ToolContractSnapshotEntry } from "./tools/contract-snapshot.ts";
+import type { DiagnosticsOperations } from "./tools/diagnostics.ts";
+import type { LspOperations } from "./tools/lsp.ts";
+import type { WebSearchOperations } from "./tools/web-search.ts";
 /** Parsed skill block from a user message */
 export interface ParsedSkillBlock {
     name: string;
@@ -141,6 +152,43 @@ export interface AgentSessionConfig {
     };
     /** Session start event metadata emitted when extensions bind to this runtime. */
     sessionStartEvent?: SessionStartEvent;
+    /**
+     * Permission gate (roadmap Phase 2a, ADR 0004). Optional and off by default: an
+     * `AgentSession` created without this is unaffected — the same behavior as
+     * before this phase. The CLI wires a real one in once a permission mode is
+     * resolved (Task 2a.7). `getContract` is not part of this config: AgentSession
+     * supplies it itself from its own tool registry, which does not exist yet at
+     * construction time — a caller cannot pass a lookup into its own future state.
+     */
+    permissionGate?: Omit<PermissionGateOptions, "getContract">;
+    /** Optional durable evidence destination. Capture remains active without any policy extension. */
+    evidenceSink?: EvidenceSink;
+    /**
+     * Optional post-mutation diagnostics (LSP.4), injected into the default `edit`/
+     * `write` tools. Absent by default -- byte-identical existing behavior. Ignored
+     * when `baseToolsOverride` is set (the caller owns tool construction then).
+     */
+    diagnosticsOperations?: DiagnosticsOperations;
+    /**
+     * Optional `lsp` navigation tool transport (LSP.5). When present, the `lsp` tool
+     * is registered and made active by default alongside read/bash/edit/write. Absent
+     * by default -- an unconfigured session's registry is unaffected. Ignored when
+     * `baseToolsOverride` is set.
+     */
+    lspOperations?: LspOperations;
+    /** Assembled MCP subsystem, present only when at least one server is configured. */
+    mcpRuntime?: McpRuntime;
+    /**
+     * Optional `web_search` backend. Absent leaves the tool on its unconfigured
+     * operations, which throw a model-readable "not configured" error rather than
+     * returning zero results. Ignored when `baseToolsOverride` is set.
+     */
+    webSearchOperations?: WebSearchOperations;
+    /**
+     * Git-backed worktree checkpoints. Absent, or present with `enabled` unset, captures
+     * nothing and runs no `git` subprocess.
+     */
+    checkpointSettings?: CheckpointSettings;
 }
 export interface ExtensionBindings {
     uiContext?: ExtensionUIContext;
@@ -152,7 +200,7 @@ export interface ExtensionBindings {
 }
 /** Options for AgentSession.prompt() */
 export interface PromptOptions {
-    /** Whether to expand file-based prompt templates (default: true) */
+    /** Whether to dispatch extension commands and expand skill commands and prompt templates (default: true) */
     expandPromptTemplates?: boolean;
     /** Image attachments */
     images?: ImageContent[];
@@ -163,6 +211,11 @@ export interface PromptOptions {
     /** Internal hook used by RPC mode to observe prompt preflight acceptance or rejection. */
     preflightResult?: (success: boolean) => void;
 }
+/** Options for model/thinking mutations. */
+export interface ModelMutationOptions {
+    /** Persist the new value to global defaults. Defaults to session-only. */
+    persist?: boolean;
+}
 /** Result from cycleModel() */
 export interface ModelCycleResult {
     model: Model<any>;
@@ -208,6 +261,7 @@ export declare class AgentSession {
     private _compactionAbortController;
     private _autoCompactionAbortController;
     private _overflowRecoveryAttempted;
+    private _midRunCompactionNeeded;
     private _branchSummaryAbortController;
     private _retryAbortController;
     private _retryAttempt;
@@ -225,6 +279,17 @@ export declare class AgentSession {
     private _excludedToolNames?;
     private _baseToolsOverride?;
     private _sessionStartEvent;
+    private _permissionGate?;
+    private _evidenceSink?;
+    private _diagnosticsOperations?;
+    private _lspOperations?;
+    private _mcpRuntime?;
+    /** Configured MCP subsystem, or undefined when no server is configured. */
+    get mcpRuntime(): McpRuntime | undefined;
+    private readonly _checkpoints;
+    /** Worktree checkpoints for this session. Inert unless `checkpoints.enabled` is set. */
+    get checkpoints(): SessionCheckpoints;
+    private _webSearchOperations?;
     private _extensionUIContext?;
     private _extensionMode;
     private _extensionCommandContextActions?;
@@ -237,6 +302,7 @@ export declare class AgentSession {
     private _toolDefinitions;
     private _toolPromptSnippets;
     private _toolPromptGuidelines;
+    private _loadedDeferredSchemas;
     private _baseSystemPrompt;
     private _baseSystemPromptOptions;
     private _systemPromptOverride?;
@@ -254,9 +320,43 @@ export declare class AgentSession {
      */
     private _installAgentToolHooks;
     private _installAgentNextTurnRefresh;
+    /** Stop an over-threshold tool loop before it sends another provider request. */
+    private _installMidRunCompactionHook;
+    private _shouldStopForMidRunCompaction;
+    /**
+     * Installs the context pipeline settled in `docs/architecture/contracts.md` § 2:
+     * deferred-schema resolution → tool-result eviction → compaction. Compaction
+     * already runs reactively from `_checkCompaction`, after a response comes back
+     * over-threshold or overflowed; this method only adds the two stages that run
+     * *ahead of* every LLM request, so that reactive check is reached less often
+     * because the request it is reacting to is smaller. It does not call into
+     * compaction and does not need to.
+     *
+     * The wiring itself — where each stage attaches, and why they land in different
+     * seams (`transformContext` for eviction, `streamFunction` for schema
+     * projection) — lives in `./context/pipeline.ts`'s `installContextPipeline`,
+     * shared with the offline replay harness so there is one implementation, not
+     * two. This method only supplies this session's two dependencies: a contract
+     * lookup backed by `getToolDefinition`, and a budget thunk (never cached — see
+     * `_evictionBudget`, which reads live `this.model` / `this.settingsManager` on
+     * every call, so a model switch or settings edit mid-session takes effect on
+     * the very next request).
+     */
+    private _installContextPipeline;
+    /**
+     * Token budget for `evictToolResults`'s outbound pass, derived from the same
+     * quantities compaction already uses for its own threshold
+     * (`getCompactionSettings()`; see `shouldCompact` in
+     * `core/compaction/compaction.ts`). The formula itself is `./context/
+     * pipeline.ts`'s `evictionBudget` — see that function's comment for the "why
+     * half of headroom" reasoning; this method only supplies production's real
+     * `contextWindow` / `reserveTokens` inputs.
+     */
+    private _evictionBudget;
     /** Emit an event to all listeners */
     private _emit;
     private _emitQueueUpdate;
+    private _emitSessionCompactFailed;
     private _getIdleWaitPromise;
     private _resolveIdleWaitIfIdle;
     private _emitAgentSettled;
@@ -303,6 +403,11 @@ export declare class AgentSession {
     /**
      * Get all configured tools with name, description, parameter schema, prompt guidelines, and source metadata.
      */
+    /**
+     * The ADR 0010 projection over this session's registry: the one read every surface
+     * that *describes* the tool set consumes. Never an authorization input.
+     */
+    getToolContractSnapshot(): ToolContractSnapshotEntry[];
     getAllTools(): ToolInfo[];
     getToolDefinition(name: string): ToolDefinition | undefined;
     /**
@@ -405,9 +510,11 @@ export declare class AgentSession {
      *
      * @param content User message content (string or content array)
      * @param options.deliverAs Delivery mode when streaming: "steer" or "followUp"
+     * @param options.expandPromptTemplates Whether to dispatch extension commands and expand skill commands and prompt templates. Default: false.
      */
     sendUserMessage(content: string | (TextContent | ImageContent)[], options?: {
         deliverAs?: "steer" | "followUp";
+        expandPromptTemplates?: boolean;
     }): Promise<void>;
     /**
      * Clear all queued messages and return them.
@@ -431,32 +538,49 @@ export declare class AgentSession {
     abort(): Promise<void>;
     waitForIdle(): Promise<void>;
     private _emitModelSelect;
+    /** True when this session runs behind a permission gate at all. */
+    get hasPermissionGate(): boolean;
+    /**
+     * The mode in force right now, and which source won. `getMode` in the gate
+     * config re-reads the store on every decision, so a mode written here applies
+     * to the next tool call with no restart.
+     */
+    getPermissionMode(): Promise<EffectiveModeResolution | undefined>;
+    /**
+     * Persist a permission mode to user scope (`~/.apex-code/agent/permissions.json`).
+     * Returns the resolution that is actually in force afterwards, which is *not*
+     * necessarily `mode`: `flag`, `local`, and `project` all outrank `user`, so the
+     * caller has to be able to tell the user their choice was recorded but shadowed.
+     */
+    setPermissionMode(mode: PermissionMode): Promise<EffectiveModeResolution | undefined>;
     /**
      * Set model directly.
-     * Validates that auth is configured, saves to session and settings.
+     * Validates that auth is configured and saves to the session transcript.
+     * Persists to global defaults only when options.persist is true.
      * @throws Error if no auth is configured for the model
      */
-    setModel(model: Model<any>): Promise<void>;
+    setModel(model: Model<any>, options?: ModelMutationOptions): Promise<void>;
     /**
      * Cycle to next/previous model.
      * Uses scoped models (from --models flag) if available, otherwise all available models.
      * @param direction - "forward" (default) or "backward"
      * @returns The new model info, or undefined if only one model available
      */
-    cycleModel(direction?: "forward" | "backward"): Promise<ModelCycleResult | undefined>;
+    cycleModel(direction?: "forward" | "backward", options?: ModelMutationOptions): Promise<ModelCycleResult | undefined>;
     private _cycleScopedModel;
     private _cycleAvailableModel;
     /**
      * Set thinking level.
      * Clamps to model capabilities based on available thinking levels.
-     * Saves to session and settings only if the level actually changes.
+     * Saves the clamped level to the session transcript only if the level actually changes.
+     * Persists the requested level to global defaults only when options.persist is true.
      */
-    setThinkingLevel(level: ThinkingLevel): void;
+    setThinkingLevel(level: ThinkingLevel, options?: ModelMutationOptions): void;
     /**
      * Cycle to next thinking level.
      * @returns New level, or undefined if model doesn't support thinking
      */
-    cycleThinkingLevel(): ThinkingLevel | undefined;
+    cycleThinkingLevel(options?: ModelMutationOptions): ThinkingLevel | undefined;
     /**
      * Get available thinking levels for current model.
      * The provider will clamp to what the specific model supports internally.
@@ -479,9 +603,20 @@ export declare class AgentSession {
      * Saves to settings.
      */
     setFollowUpMode(mode: "all" | "one-at-a-time"): void;
+    private _runDefaultCompaction;
     /**
      * Manually compact the session context.
-     * Aborts current agent operation first.
+     *
+     * This is the manual entry point used by `/compact`, RPC, and extensions. It is
+     * separate from automatic threshold/overflow compaction, which enters through
+     * `_checkCompaction()` and `_runAutoCompaction()`. After preparation and the
+     * `session_before_compact` hook, both paths call the lower-level `compact()`
+     * function imported from `./compaction/index.ts`, unless the hook cancels or
+     * supplies a custom result.
+     *
+     * Aborts the current agent operation first. Manual compaction never retries or
+     * continues the interrupted agent turn.
+     *
      * @param customInstructions Optional instructions for the compaction summary
      */
     compact(customInstructions?: string): Promise<CompactionResult>;
@@ -615,9 +750,12 @@ export declare class AgentSession {
     /**
      * Export session to HTML.
      * @param outputPath Optional output path (defaults to session directory)
+     * @param options Optional export presentation settings
      * @returns Path to exported file
      */
-    exportToHtml(outputPath?: string): Promise<string>;
+    exportToHtml(outputPath?: string, options?: {
+        themeName?: string;
+    }): Promise<string>;
     /**
      * Export the current session branch to a JSONL file.
      * Writes the session header followed by all entries on the current branch path.