@caupulican/pi-adaptative 0.81.38 → 0.81.40

package/dist/migrations.d.ts

@@ -18,6 +18,13 @@ export declare function migrateAuthToAuthJson(): string[];
  */
 export declare function getMigratedSessionFileName(file: string): string | undefined;
 export declare function migrateSessionsFromAgentRoot(): void;
+/** Remove only empty real per-project session directories; transcript files are never retention-pruned. */
+export declare function pruneEmptySessionNamespaces(agentDir: string): string[];
+/**
+ * Consolidate known machine-managed layout generations. Each migration is independently guarded:
+ * startup never fails because cleanup is unavailable, and unknown files/resources remain untouched.
+ */
+export declare function migrateAgentDirLayout(agentDir: string): void;
 /**
  * Print deprecation warnings and wait for keypress.
  */

package/dist/migrations.d.ts.map

@@ -1 +1 @@
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`$${value}` : undefined;\n}\n\nfunction migrateStringProperty(\n\trecord: Record<string, unknown>,\n\tkey: string,\n\tlocation: string,\n\tmigrations: ConfigValueMigration[],\n): boolean {\n\tconst value = record[key];\n\tif (typeof value !== \"string\") return false;\n\tconst migrated = migrateLegacyEnvVarString(value);\n\tif (migrated === undefined) return false;\n\trecord[key] = migrated;\n\tmigrations.push({ location, from: value, to: migrated });\n\treturn true;\n}\n\nfunction migrateHeadersConfig(headers: unknown, location: string, migrations: ConfigValueMigration[]): boolean {\n\tif (typeof headers !== \"object\" || headers === null || Array.isArray(headers)) return false;\n\tconst headerRecord = headers as Record<string, unknown>;\n\tlet migrated = false;\n\tfor (const [key, value] of Object.entries(headerRecord)) {\n\t\tif (typeof value !== \"string\") continue;\n\t\tconst migratedValue = migrateLegacyEnvVarString(value);\n\t\tif (migratedValue === undefined) continue;\n\t\theaderRecord[key] = migratedValue;\n\t\tmigrations.push({ location: `${location}[${JSON.stringify(key)}]`, from: value, to: migratedValue });\n\t\tmigrated = true;\n\t}\n\treturn migrated;\n}\n\nfunction migrateAuthJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst authPath = join(agentDir, \"auth.json\");\n\tif (!existsSync(authPath)) return [];\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(authPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\t\tconst authData = parsed as Record<string, unknown>;\n\n\t\tconst migrations: ConfigValueMigration[] = [];\n\t\tfor (const [provider, credential] of Object.entries(authData)) {\n\t\t\tif (typeof credential !== \"object\" || credential === null || Array.isArray(credential)) continue;\n\t\t\tconst credentialRecord = credential as Record<string, unknown>;\n\t\t\tif (credentialRecord.type !== \"api_key\") continue;\n\t\t\tmigrateStringProperty(credentialRecord, \"key\", `auth.json[${JSON.stringify(provider)}].key`, migrations);\n\t\t}\n\n\t\tif (migrations.length === 0) return [];\n\t\twriteFileSync(authPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\t\tchmodSync(authPath, 0o600);\n\t\treturn migrations;\n\t} catch {\n\t\treturn [];\n\t}\n}\n\nfunction migrateModelsJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst modelsPath = join(agentDir, \"models.json\");\n\tif (!existsSync(modelsPath)) return [];\n\n\tlet parsed: unknown;\n\ttry {\n\t\tparsed = JSON.parse(stripJsonComments(readFileSync(modelsPath, \"utf-8\"))) as unknown;\n\t} catch {\n\t\treturn [];\n\t}\n\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\tconst modelsData = parsed as Record<string, unknown>;\n\tconst providers = modelsData.providers;\n\tif (typeof providers !== \"object\" || providers === null || Array.isArray(providers)) return [];\n\n\tconst migrations: ConfigValueMigration[] = [];\n\tfor (const [provider, providerConfig] of Object.entries(providers)) {\n\t\tif (typeof providerConfig !== \"object\" || providerConfig === null || Array.isArray(providerConfig)) continue;\n\t\tconst providerRecord = providerConfig as Record<string, unknown>;\n\t\tconst providerLocation = `models.json.providers[${JSON.stringify(provider)}]`;\n\t\tmigrateStringProperty(providerRecord, \"apiKey\", `${providerLocation}.apiKey`, migrations);\n\t\tmigrateHeadersConfig(providerRecord.headers, `${providerLocation}.headers`, migrations);\n\n\t\tif (Array.isArray(providerRecord.models)) {\n\t\t\tfor (let index = 0; index < providerRecord.models.length; index++) {\n\t\t\t\tconst modelConfig = providerRecord.models[index];\n\t\t\t\tif (typeof modelConfig !== \"object\" || modelConfig === null || Array.isArray(modelConfig)) continue;\n\t\t\t\tconst modelRecord = modelConfig as Record<string, unknown>;\n\t\t\t\tconst modelKey = typeof modelRecord.id === \"string\" ? JSON.stringify(modelRecord.id) : String(index);\n\t\t\t\tmigrateHeadersConfig(modelRecord.headers, `${providerLocation}.models[${modelKey}].headers`, migrations);\n\t\t\t}\n\t\t}\n\n\t\tconst modelOverrides = providerRecord.modelOverrides;\n\t\tif (typeof modelOverrides === \"object\" && modelOverrides !== null && !Array.isArray(modelOverrides)) {\n\t\t\tfor (const [modelId, modelOverride] of Object.entries(modelOverrides)) {\n\t\t\t\tif (typeof modelOverride !== \"object\" || modelOverride === null || Array.isArray(modelOverride)) continue;\n\t\t\t\tconst modelOverrideRecord = modelOverride as Record<string, unknown>;\n\t\t\t\tmigrateHeadersConfig(\n\t\t\t\t\tmodelOverrideRecord.headers,\n\t\t\t\t\t`${providerLocation}.modelOverrides[${JSON.stringify(modelId)}].headers`,\n\t\t\t\t\tmigrations,\n\t\t\t\t);\n\t\t\t}\n\t\t}\n\t}\n\n\tif (migrations.length === 0) return [];\n\twriteFileSync(modelsPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\treturn migrations;\n}\n\nfunction migrateExplicitEnvVarConfigValues(): void {\n\tconst agentDir = getAgentDir();\n\tconst migrations = [...migrateAuthJsonConfigValues(agentDir), ...migrateModelsJsonConfigValues(agentDir)];\n\tif (migrations.length === 0) return;\n\n\tconst details = migrations.map((migration) => `  - ${migration.location}: ${migration.from} -> ${migration.to}`);\n\tconsole.log(\n\t\tchalk.yellow(\n\t\t\t[\n\t\t\t\t\"Warning: Migrated API key/header environment references to explicit $ENV_VAR syntax. Plain strings will be treated as literals.\",\n\t\t\t\t...details,\n\t\t\t].join(\"\\n\"),\n\t\t),\n\t);\n}\n\n/**\n * Migrate sessions from ~/.pi/agent/*.jsonl to proper session directories.\n *\n * Bug in v0.30.0: Sessions were saved to ~/.pi/agent/ instead of\n * ~/.pi/agent/sessions/<encoded-cwd>/. This migration moves them\n * to the correct location based on the cwd in their session header.\n *\n * See: https://github.com/earendil-works/pi-mono/issues/320\n */\nexport function getMigratedSessionFileName(file: string): string | undefined {\n\tconst fileName = file.split(/[\\\\/]/).pop();\n\treturn fileName || undefined;\n}\n\nexport function migrateSessionsFromAgentRoot(): void {\n\tconst agentDir = getAgentDir();\n\n\t// Find all .jsonl files directly in agentDir (not in subdirectories)\n\tlet files: string[];\n\ttry {\n\t\tfiles = readdirSync(agentDir)\n\t\t\t.filter((f) => f.endsWith(\".jsonl\"))\n\t\t\t.map((f) => join(agentDir, f));\n\t} catch {\n\t\treturn;\n\t}\n\n\tif (files.length === 0) return;\n\n\tfor (const file of files) {\n\t\ttry {\n\t\t\t// Read first line to get session header\n\t\t\tconst content = readFileSync(file, \"utf8\");\n\t\t\tconst firstLine = content.split(\"\\n\")[0];\n\t\t\tif (!firstLine?.trim()) continue;\n\n\t\t\tconst header = JSON.parse(firstLine);\n\t\t\tif (header.type !== \"session\" || !header.cwd) continue;\n\n\t\t\tconst cwd: string = header.cwd;\n\n\t\t\t// Compute the correct session directory (same encoding as session-manager.ts)\n\t\t\tconst safePath = `--${cwd.replace(/^[/\\\\]/, \"\").replace(/[/\\\\:]/g, \"-\")}--`;\n\t\t\tconst correctDir = join(agentDir, \"sessions\", safePath);\n\n\t\t\t// Create directory if needed\n\t\t\tif (!existsSync(correctDir)) {\n\t\t\t\tmkdirSync(correctDir, { recursive: true });\n\t\t\t}\n\n\t\t\t// Move the file\n\t\t\tconst fileName = getMigratedSessionFileName(file);\n\t\t\tif (!fileName) continue;\n\t\t\tconst newPath = join(correctDir, fileName);\n\n\t\t\tif (existsSync(newPath)) continue; // Skip if target exists\n\n\t\t\trenameSync(file, newPath);\n\t\t} catch {\n\t\t\t// Skip files that can't be migrated\n\t\t}\n\t}\n}\n\n/**\n * Migrate commands/ to prompts/ if needed.\n * Works for both regular directories and symlinks.\n */\nfunction migrateCommandsToPrompts(baseDir: string, label: string): boolean {\n\tconst commandsDir = join(baseDir, \"commands\");\n\tconst promptsDir = join(baseDir, \"prompts\");\n\n\tif (existsSync(commandsDir) && !existsSync(promptsDir)) {\n\t\ttry {\n\t\t\trenameSync(commandsDir, promptsDir);\n\t\t\tconsole.log(chalk.green(`Migrated ${label} commands/ → prompts/`));\n\t\t\treturn true;\n\t\t} catch (err) {\n\t\t\tconsole.log(\n\t\t\t\tchalk.yellow(\n\t\t\t\t\t`Warning: Could not migrate ${label} commands/ to prompts/: ${err instanceof Error ? err.message : err}`,\n\t\t\t\t),\n\t\t\t);\n\t\t}\n\t}\n\treturn false;\n}\n\nfunction migrateKeybindingsConfigFile(): void {\n\tconst configPath = join(getAgentDir(), \"keybindings.json\");\n\tif (!existsSync(configPath)) return;\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(configPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) {\n\t\t\treturn;\n\t\t}\n\t\tconst { config, migrated } = migrateKeybindingsConfig(parsed as Record<string, unknown>);\n\t\tif (!migrated) return;\n\t\twriteFileSync(configPath, `${JSON.stringify(config, null, 2)}\\n`, \"utf-8\");\n\t} catch {\n\t\t// Ignore malformed files during migration\n\t}\n}\n\n/**\n * Move fd/rg binaries from tools/ to bin/ if they exist.\n */\nfunction migrateToolsToBin(): void {\n\tconst agentDir = getAgentDir();\n\tconst toolsDir = join(agentDir, \"tools\");\n\tconst binDir = getBinDir();\n\n\tif (!existsSync(toolsDir)) return;\n\n\tconst binaries = [\"fd\", \"rg\", \"fd.exe\", \"rg.exe\"];\n\tlet movedAny = false;\n\n\tfor (const bin of binaries) {\n\t\tconst oldPath = join(toolsDir, bin);\n\t\tconst newPath = join(binDir, bin);\n\n\t\tif (existsSync(oldPath)) {\n\t\t\tif (!existsSync(binDir)) {\n\t\t\t\tmkdirSync(binDir, { recursive: true });\n\t\t\t}\n\t\t\tif (!existsSync(newPath)) {\n\t\t\t\ttry {\n\t\t\t\t\trenameSync(oldPath, newPath);\n\t\t\t\t\tmovedAny = true;\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore errors\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// Target exists, just delete the old one\n\t\t\t\ttry {\n\t\t\t\t\trmSync?.(oldPath, { force: true });\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tif (movedAny) {\n\t\tconsole.log(chalk.green(`Migrated managed binaries tools/ → bin/`));\n\t}\n}\n\n/**\n * Check for deprecated hooks/ and tools/ directories.\n * Note: tools/ may contain fd/rg binaries extracted by pi, so only warn if it has other files.\n */\nfunction checkDeprecatedExtensionDirs(baseDir: string, label: string): string[] {\n\tconst hooksDir = join(baseDir, \"hooks\");\n\tconst toolsDir = join(baseDir, \"tools\");\n\tconst warnings: string[] = [];\n\n\tif (existsSync(hooksDir)) {\n\t\twarnings.push(`${label} hooks/ directory found. Hooks have been renamed to extensions.`);\n\t}\n\n\tif (existsSync(toolsDir)) {\n\t\t// Check if tools/ contains anything other than fd/rg (which are auto-extracted binaries)\n\t\ttry {\n\t\t\tconst entries = readdirSync(toolsDir);\n\t\t\tconst customTools = entries.filter((e) => {\n\t\t\t\tconst lower = e.toLowerCase();\n\t\t\t\treturn (\n\t\t\t\t\tlower !== \"fd\" && lower !== \"rg\" && lower !== \"fd.exe\" && lower !== \"rg.exe\" && !e.startsWith(\".\") // Ignore .DS_Store and other hidden files\n\t\t\t\t);\n\t\t\t});\n\t\t\tif (customTools.length > 0) {\n\t\t\t\twarnings.push(\n\t\t\t\t\t`${label} tools/ directory contains custom tools. Custom tools have been merged into extensions.`,\n\t\t\t\t);\n\t\t\t}\n\t\t} catch {\n\t\t\t// Ignore read errors\n\t\t}\n\t}\n\n\treturn warnings;\n}\n\n/**\n * Run extension system migrations (commands→prompts) and collect warnings about deprecated directories.\n */\nfunction migrateExtensionSystem(cwd: string): string[] {\n\tconst agentDir = getAgentDir();\n\tconst projectDir = join(cwd, CONFIG_DIR_NAME);\n\n\t// Migrate commands/ to prompts/\n\tmigrateCommandsToPrompts(agentDir, \"Global\");\n\tmigrateCommandsToPrompts(projectDir, \"Project\");\n\n\t// Check for deprecated directories\n\tconst warnings = [\n\t\t...checkDeprecatedExtensionDirs(agentDir, \"Global\"),\n\t\t...checkDeprecatedExtensionDirs(projectDir, \"Project\"),\n\t];\n\n\treturn warnings;\n}\n\n/**\n * Print deprecation warnings and wait for keypress.\n */\nexport async function showDeprecationWarnings(warnings: string[]): Promise<void> {\n\tif (warnings.length === 0) return;\n\n\tfor (const warning of warnings) {\n\t\tconsole.log(chalk.yellow(`Warning: ${warning}`));\n\t}\n\tconsole.log(chalk.yellow(`\\nMove your extensions to the extensions/ directory.`));\n\tconsole.log(chalk.yellow(`Migration guide: ${MIGRATION_GUIDE_URL}`));\n\tconsole.log(chalk.yellow(`Documentation: ${EXTENSIONS_DOC_URL}`));\n\tif (!process.stdin.isTTY || !process.stdout.isTTY) {\n\t\tconsole.log();\n\t\treturn;\n\t}\n\tconsole.log(chalk.dim(`\\nPress any key to continue...`));\n\n\tawait new Promise<void>((resolve) => {\n\t\tlet settled = false;\n\t\tconst finish = () => {\n\t\t\tif (settled) return;\n\t\t\tsettled = true;\n\t\t\tprocess.stdin.removeListener(\"data\", finish);\n\t\t\tprocess.stdin.removeListener(\"end\", finish);\n\t\t\tprocess.stdin.removeListener(\"error\", finish);\n\t\t\tprocess.stdin.setRawMode?.(false);\n\t\t\tprocess.stdin.pause();\n\t\t\tresolve();\n\t\t};\n\t\tprocess.stdin.setRawMode?.(true);\n\t\tprocess.stdin.resume();\n\t\tprocess.stdin.once(\"data\", finish);\n\t\tprocess.stdin.once(\"end\", finish);\n\t\tprocess.stdin.once(\"error\", finish);\n\t});\n\tconsole.log();\n}\n\n/**\n * Run all migrations. Called once on startup.\n *\n * @returns Object with migration results and deprecation warnings\n */\nexport function runMigrations(cwd: string): {\n\tmigratedAuthProviders: string[];\n\tdeprecationWarnings: string[];\n} {\n\tconst migratedAuthProviders = migrateAuthToAuthJson();\n\tmigrateExplicitEnvVarConfigValues();\n\tmigrateSessionsFromAgentRoot();\n\tmigrateToolsToBin();\n\tmigrateKeybindingsConfigFile();\n\tconst deprecationWarnings = migrateExtensionSystem(cwd);\n\treturn { migratedAuthProviders, deprecationWarnings };\n}\n"]}
+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../src/migrations.ts"],"names":[],"mappings":"AAAA;;GAEG;AA8BH;;;;GAIG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,EAAE,CAoDhD;AAwID;;;;;;;;GAQG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAG3E;AAED,wBAAgB,4BAA4B,IAAI,IAAI,CAgDnD;AAiND,2GAA2G;AAC3G,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAsBtE;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,CA8B5D;AA0DD;;GAEG;AACH,wBAAsB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAkC/E;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG;IAC3C,qBAAqB,EAAE,MAAM,EAAE,CAAC;IAChC,mBAAmB,EAAE,MAAM,EAAE,CAAC;CAC9B,CASA","sourcesContent":["/**\n * One-time migrations that run on startup.\n */\n\nimport chalk from \"chalk\";\nimport {\n\tchmodSync,\n\texistsSync,\n\tlstatSync,\n\tmkdirSync,\n\treaddirSync,\n\treadFileSync,\n\trenameSync,\n\trmdirSync,\n\trmSync,\n\tunlinkSync,\n\twriteFileSync,\n} from \"fs\";\nimport { dirname, join } from \"path\";\nimport { CONFIG_DIR_NAME, getAgentDir, getBinDir } from \"./config.ts\";\nimport { configBackupsDir, directoryProfilesDir, sessionsDir, stateFile } from \"./core/agent-paths.ts\";\nimport { migrateLegacyContextStores, pruneContextStores } from \"./core/context/context-store-retention.ts\";\nimport { migrateKeybindingsConfig } from \"./core/keybindings.ts\";\nimport { isLegacyEnvVarNameConfigValue } from \"./core/resolve-config-value.ts\";\nimport { withFileLockSync, writeFileAtomicSync } from \"./core/util/atomic-file.ts\";\nimport { stripJsonComments } from \"./utils/json.ts\";\n\nconst MIGRATION_GUIDE_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/CHANGELOG.md#extensions-migration\";\nconst EXTENSIONS_DOC_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/docs/extensions.md\";\n\n/**\n * Migrate legacy oauth.json and settings.json apiKeys to auth.json.\n *\n * @returns Array of provider names that were migrated\n */\nexport function migrateAuthToAuthJson(): string[] {\n\tconst agentDir = getAgentDir();\n\tconst authPath = join(agentDir, \"auth.json\");\n\tconst oauthPath = join(agentDir, \"oauth.json\");\n\tconst settingsPath = join(agentDir, \"settings.json\");\n\n\t// Skip if auth.json already exists\n\tif (existsSync(authPath)) return [];\n\n\tconst migrated: Record<string, unknown> = {};\n\tconst providers: string[] = [];\n\n\t// Migrate oauth.json\n\tif (existsSync(oauthPath)) {\n\t\ttry {\n\t\t\tconst oauth = JSON.parse(readFileSync(oauthPath, \"utf-8\"));\n\t\t\tfor (const [provider, cred] of Object.entries(oauth)) {\n\t\t\t\tmigrated[provider] = { type: \"oauth\", ...(cred as object) };\n\t\t\t\tproviders.push(provider);\n\t\t\t}\n\t\t\trenameSync(oauthPath, `${oauthPath}.migrated`);\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\t// Migrate settings.json apiKeys\n\tif (existsSync(settingsPath)) {\n\t\ttry {\n\t\t\tconst content = readFileSync(settingsPath, \"utf-8\");\n\t\t\tconst settings = JSON.parse(content);\n\t\t\tif (settings.apiKeys && typeof settings.apiKeys === \"object\") {\n\t\t\t\tfor (const [provider, key] of Object.entries(settings.apiKeys)) {\n\t\t\t\t\tif (!migrated[provider] && typeof key === \"string\") {\n\t\t\t\t\t\tmigrated[provider] = { type: \"api_key\", key };\n\t\t\t\t\t\tproviders.push(provider);\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tdelete settings.apiKeys;\n\t\t\t\twriteFileSync(settingsPath, JSON.stringify(settings, null, 2));\n\t\t\t}\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\tif (Object.keys(migrated).length > 0) {\n\t\tmkdirSync(dirname(authPath), { recursive: true });\n\t\twriteFileSync(authPath, JSON.stringify(migrated, null, 2), { mode: 0o600 });\n\t}\n\n\treturn providers;\n}\n\ninterface ConfigValueMigration {\n\tlocation: string;\n\tfrom: string;\n\tto: string;\n}\n\nfunction migrateLegacyEnvVarString(value: string): string | undefined {\n\treturn isLegacyEnvVarNameConfigValue(value) ? `$${value}` : undefined;\n}\n\nfunction migrateStringProperty(\n\trecord: Record<string, unknown>,\n\tkey: string,\n\tlocation: string,\n\tmigrations: ConfigValueMigration[],\n): boolean {\n\tconst value = record[key];\n\tif (typeof value !== \"string\") return false;\n\tconst migrated = migrateLegacyEnvVarString(value);\n\tif (migrated === undefined) return false;\n\trecord[key] = migrated;\n\tmigrations.push({ location, from: value, to: migrated });\n\treturn true;\n}\n\nfunction migrateHeadersConfig(headers: unknown, location: string, migrations: ConfigValueMigration[]): boolean {\n\tif (typeof headers !== \"object\" || headers === null || Array.isArray(headers)) return false;\n\tconst headerRecord = headers as Record<string, unknown>;\n\tlet migrated = false;\n\tfor (const [key, value] of Object.entries(headerRecord)) {\n\t\tif (typeof value !== \"string\") continue;\n\t\tconst migratedValue = migrateLegacyEnvVarString(value);\n\t\tif (migratedValue === undefined) continue;\n\t\theaderRecord[key] = migratedValue;\n\t\tmigrations.push({ location: `${location}[${JSON.stringify(key)}]`, from: value, to: migratedValue });\n\t\tmigrated = true;\n\t}\n\treturn migrated;\n}\n\nfunction migrateAuthJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst authPath = join(agentDir, \"auth.json\");\n\tif (!existsSync(authPath)) return [];\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(authPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\t\tconst authData = parsed as Record<string, unknown>;\n\n\t\tconst migrations: ConfigValueMigration[] = [];\n\t\tfor (const [provider, credential] of Object.entries(authData)) {\n\t\t\tif (typeof credential !== \"object\" || credential === null || Array.isArray(credential)) continue;\n\t\t\tconst credentialRecord = credential as Record<string, unknown>;\n\t\t\tif (credentialRecord.type !== \"api_key\") continue;\n\t\t\tmigrateStringProperty(credentialRecord, \"key\", `auth.json[${JSON.stringify(provider)}].key`, migrations);\n\t\t}\n\n\t\tif (migrations.length === 0) return [];\n\t\twriteFileSync(authPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\t\tchmodSync(authPath, 0o600);\n\t\treturn migrations;\n\t} catch {\n\t\treturn [];\n\t}\n}\n\nfunction migrateModelsJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst modelsPath = join(agentDir, \"models.json\");\n\tif (!existsSync(modelsPath)) return [];\n\n\tlet parsed: unknown;\n\ttry {\n\t\tparsed = JSON.parse(stripJsonComments(readFileSync(modelsPath, \"utf-8\"))) as unknown;\n\t} catch {\n\t\treturn [];\n\t}\n\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\tconst modelsData = parsed as Record<string, unknown>;\n\tconst providers = modelsData.providers;\n\tif (typeof providers !== \"object\" || providers === null || Array.isArray(providers)) return [];\n\n\tconst migrations: ConfigValueMigration[] = [];\n\tfor (const [provider, providerConfig] of Object.entries(providers)) {\n\t\tif (typeof providerConfig !== \"object\" || providerConfig === null || Array.isArray(providerConfig)) continue;\n\t\tconst providerRecord = providerConfig as Record<string, unknown>;\n\t\tconst providerLocation = `models.json.providers[${JSON.stringify(provider)}]`;\n\t\tmigrateStringProperty(providerRecord, \"apiKey\", `${providerLocation}.apiKey`, migrations);\n\t\tmigrateHeadersConfig(providerRecord.headers, `${providerLocation}.headers`, migrations);\n\n\t\tif (Array.isArray(providerRecord.models)) {\n\t\t\tfor (let index = 0; index < providerRecord.models.length; index++) {\n\t\t\t\tconst modelConfig = providerRecord.models[index];\n\t\t\t\tif (typeof modelConfig !== \"object\" || modelConfig === null || Array.isArray(modelConfig)) continue;\n\t\t\t\tconst modelRecord = modelConfig as Record<string, unknown>;\n\t\t\t\tconst modelKey = typeof modelRecord.id === \"string\" ? JSON.stringify(modelRecord.id) : String(index);\n\t\t\t\tmigrateHeadersConfig(modelRecord.headers, `${providerLocation}.models[${modelKey}].headers`, migrations);\n\t\t\t}\n\t\t}\n\n\t\tconst modelOverrides = providerRecord.modelOverrides;\n\t\tif (typeof modelOverrides === \"object\" && modelOverrides !== null && !Array.isArray(modelOverrides)) {\n\t\t\tfor (const [modelId, modelOverride] of Object.entries(modelOverrides)) {\n\t\t\t\tif (typeof modelOverride !== \"object\" || modelOverride === null || Array.isArray(modelOverride)) continue;\n\t\t\t\tconst modelOverrideRecord = modelOverride as Record<string, unknown>;\n\t\t\t\tmigrateHeadersConfig(\n\t\t\t\t\tmodelOverrideRecord.headers,\n\t\t\t\t\t`${providerLocation}.modelOverrides[${JSON.stringify(modelId)}].headers`,\n\t\t\t\t\tmigrations,\n\t\t\t\t);\n\t\t\t}\n\t\t}\n\t}\n\n\tif (migrations.length === 0) return [];\n\twriteFileSync(modelsPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\treturn migrations;\n}\n\nfunction migrateExplicitEnvVarConfigValues(): void {\n\tconst agentDir = getAgentDir();\n\tconst migrations = [...migrateAuthJsonConfigValues(agentDir), ...migrateModelsJsonConfigValues(agentDir)];\n\tif (migrations.length === 0) return;\n\n\tconst details = migrations.map((migration) => `  - ${migration.location}: ${migration.from} -> ${migration.to}`);\n\tconsole.log(\n\t\tchalk.yellow(\n\t\t\t[\n\t\t\t\t\"Warning: Migrated API key/header environment references to explicit $ENV_VAR syntax. Plain strings will be treated as literals.\",\n\t\t\t\t...details,\n\t\t\t].join(\"\\n\"),\n\t\t),\n\t);\n}\n\n/**\n * Migrate sessions from ~/.pi/agent/*.jsonl to proper session directories.\n *\n * Bug in v0.30.0: Sessions were saved to ~/.pi/agent/ instead of\n * ~/.pi/agent/sessions/<encoded-cwd>/. This migration moves them\n * to the correct location based on the cwd in their session header.\n *\n * See: https://github.com/earendil-works/pi-mono/issues/320\n */\nexport function getMigratedSessionFileName(file: string): string | undefined {\n\tconst fileName = file.split(/[\\\\/]/).pop();\n\treturn fileName || undefined;\n}\n\nexport function migrateSessionsFromAgentRoot(): void {\n\tconst agentDir = getAgentDir();\n\n\t// Find all .jsonl files directly in agentDir (not in subdirectories)\n\tlet files: string[];\n\ttry {\n\t\tfiles = readdirSync(agentDir)\n\t\t\t.filter((f) => f.endsWith(\".jsonl\"))\n\t\t\t.map((f) => join(agentDir, f));\n\t} catch {\n\t\treturn;\n\t}\n\n\tif (files.length === 0) return;\n\n\tfor (const file of files) {\n\t\ttry {\n\t\t\t// Read first line to get session header\n\t\t\tconst content = readFileSync(file, \"utf8\");\n\t\t\tconst firstLine = content.split(\"\\n\")[0];\n\t\t\tif (!firstLine?.trim()) continue;\n\n\t\t\tconst header = JSON.parse(firstLine);\n\t\t\tif (header.type !== \"session\" || !header.cwd) continue;\n\n\t\t\tconst cwd: string = header.cwd;\n\n\t\t\t// Compute the correct session directory (same encoding as session-manager.ts)\n\t\t\tconst safePath = `--${cwd.replace(/^[/\\\\]/, \"\").replace(/[/\\\\:]/g, \"-\")}--`;\n\t\t\tconst correctDir = join(agentDir, \"sessions\", safePath);\n\n\t\t\t// Create directory if needed\n\t\t\tif (!existsSync(correctDir)) {\n\t\t\t\tmkdirSync(correctDir, { recursive: true });\n\t\t\t}\n\n\t\t\t// Move the file\n\t\t\tconst fileName = getMigratedSessionFileName(file);\n\t\t\tif (!fileName) continue;\n\t\t\tconst newPath = join(correctDir, fileName);\n\n\t\t\tif (existsSync(newPath)) continue; // Skip if target exists\n\n\t\t\trenameSync(file, newPath);\n\t\t} catch {\n\t\t\t// Skip files that can't be migrated\n\t\t}\n\t}\n}\n\n/**\n * Migrate commands/ to prompts/ if needed.\n * Works for both regular directories and symlinks.\n */\nfunction migrateCommandsToPrompts(baseDir: string, label: string): boolean {\n\tconst commandsDir = join(baseDir, \"commands\");\n\tconst promptsDir = join(baseDir, \"prompts\");\n\n\tif (existsSync(commandsDir) && !existsSync(promptsDir)) {\n\t\ttry {\n\t\t\trenameSync(commandsDir, promptsDir);\n\t\t\tconsole.log(chalk.green(`Migrated ${label} commands/ → prompts/`));\n\t\t\treturn true;\n\t\t} catch (err) {\n\t\t\tconsole.log(\n\t\t\t\tchalk.yellow(\n\t\t\t\t\t`Warning: Could not migrate ${label} commands/ to prompts/: ${err instanceof Error ? err.message : err}`,\n\t\t\t\t),\n\t\t\t);\n\t\t}\n\t}\n\treturn false;\n}\n\nfunction migrateKeybindingsConfigFile(): void {\n\tconst configPath = join(getAgentDir(), \"keybindings.json\");\n\tif (!existsSync(configPath)) return;\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(configPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) {\n\t\t\treturn;\n\t\t}\n\t\tconst { config, migrated } = migrateKeybindingsConfig(parsed as Record<string, unknown>);\n\t\tif (!migrated) return;\n\t\twriteFileSync(configPath, `${JSON.stringify(config, null, 2)}\\n`, \"utf-8\");\n\t} catch {\n\t\t// Ignore malformed files during migration\n\t}\n}\n\n/**\n * Move fd/rg binaries from tools/ to bin/ if they exist.\n */\nfunction migrateToolsToBin(): void {\n\tconst agentDir = getAgentDir();\n\tconst toolsDir = join(agentDir, \"tools\");\n\tconst binDir = getBinDir();\n\n\tif (!existsSync(toolsDir)) return;\n\n\tconst binaries = [\"fd\", \"rg\", \"fd.exe\", \"rg.exe\"];\n\tlet movedAny = false;\n\n\tfor (const bin of binaries) {\n\t\tconst oldPath = join(toolsDir, bin);\n\t\tconst newPath = join(binDir, bin);\n\n\t\tif (existsSync(oldPath)) {\n\t\t\tif (!existsSync(binDir)) {\n\t\t\t\tmkdirSync(binDir, { recursive: true });\n\t\t\t}\n\t\t\tif (!existsSync(newPath)) {\n\t\t\t\ttry {\n\t\t\t\t\trenameSync(oldPath, newPath);\n\t\t\t\t\tmovedAny = true;\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore errors\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// Target exists, just delete the old one\n\t\t\t\ttry {\n\t\t\t\t\trmSync?.(oldPath, { force: true });\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tif (movedAny) {\n\t\tconsole.log(chalk.green(`Migrated managed binaries tools/ → bin/`));\n\t}\n}\n\n/**\n * Root-level machine-managed trust state is relocated into `state/`. If both layouts exist, valid\n * entries are merged under the canonical file's lock and canonical decisions win conflicts.\n */\nconst MAX_SESSION_NAMESPACES_TO_PRUNE = 10_000;\nconst MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE = 10_000;\nconst MAX_MIGRATION_CONFLICT_SUFFIXES = 1_000;\n\ntype MigratedTrustFile = Record<string, boolean | null>;\n\nfunction readMigratedTrustFile(path: string): MigratedTrustFile | undefined {\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(path, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return undefined;\n\t\tconst trust: MigratedTrustFile = {};\n\t\tfor (const [key, value] of Object.entries(parsed)) {\n\t\t\tif (value !== true && value !== false && value !== null) return undefined;\n\t\t\ttrust[key] = value;\n\t\t}\n\t\treturn trust;\n\t} catch {\n\t\treturn undefined;\n\t}\n}\n\nfunction migrateTrustState(agentDir: string): void {\n\tconst oldPath = join(agentDir, \"trust.json\");\n\tif (!existsSync(oldPath)) return;\n\tconst newPath = stateFile(agentDir, \"trust.json\");\n\tif (!existsSync(newPath)) {\n\t\tmkdirSync(dirname(newPath), { recursive: true });\n\t\trenameSync(oldPath, newPath);\n\t\treturn;\n\t}\n\n\twithFileLockSync(newPath, () => {\n\t\tconst legacy = readMigratedTrustFile(oldPath);\n\t\tconst canonical = readMigratedTrustFile(newPath);\n\t\tif (!legacy || !canonical) return;\n\t\tconst merged = { ...legacy, ...canonical };\n\t\tconst sorted = Object.fromEntries(Object.entries(merged).sort(([left], [right]) => left.localeCompare(right)));\n\t\twriteFileAtomicSync(newPath, `${JSON.stringify(sorted, null, 2)}\\n`);\n\t\tunlinkSync(oldPath);\n\t});\n}\n\nfunction migrationConflictPath(agentDir: string, legacyName: string, entryName: string): string | undefined {\n\tconst conflictDir = stateFile(agentDir, \"migration-conflicts\", legacyName);\n\tfor (let suffix = 0; suffix < MAX_MIGRATION_CONFLICT_SUFFIXES; suffix++) {\n\t\tconst name = suffix === 0 ? entryName : `${entryName}.legacy-${suffix}`;\n\t\tconst candidate = join(conflictDir, name);\n\t\tif (!existsSync(candidate)) return candidate;\n\t}\n\treturn undefined;\n}\n\n/**\n * Relocate one known legacy root without traversing its contents. A whole-root rename is O(1);\n * partial migrations scan a bounded number of top-level entries and preserve collisions under\n * state/migration-conflicts instead of overwriting either copy.\n */\nfunction migrateLegacyAgentDirectory(agentDir: string, legacyName: string, canonicalDir: string): void {\n\tconst legacyDir = join(agentDir, legacyName);\n\tif (!existsSync(legacyDir)) return;\n\tconst legacyStats = lstatSync(legacyDir);\n\tif (!legacyStats.isDirectory() || legacyStats.isSymbolicLink()) return;\n\n\tif (!existsSync(canonicalDir)) {\n\t\tmkdirSync(dirname(canonicalDir), { recursive: true });\n\t\trenameSync(legacyDir, canonicalDir);\n\t\treturn;\n\t}\n\n\tconst canonicalStats = lstatSync(canonicalDir);\n\tif (!canonicalStats.isDirectory() || canonicalStats.isSymbolicLink()) return;\n\tconst entries = readdirSync(legacyDir).slice(0, MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE);\n\tfor (const entry of entries) {\n\t\tconst source = join(legacyDir, entry);\n\t\tlet target = join(canonicalDir, entry);\n\t\tif (existsSync(target)) {\n\t\t\ttarget = migrationConflictPath(agentDir, legacyName, entry) ?? \"\";\n\t\t\tif (!target) continue;\n\t\t\tmkdirSync(dirname(target), { recursive: true });\n\t\t}\n\t\ttry {\n\t\t\trenameSync(source, target);\n\t\t} catch {}\n\t}\n\n\ttry {\n\t\trmdirSync(legacyDir);\n\t} catch {}\n}\n\nfunction migrateLegacyAgentFile(agentDir: string, legacyName: string, canonicalPath: string): void {\n\tconst legacyPath = join(agentDir, legacyName);\n\tif (!existsSync(legacyPath)) return;\n\tconst legacyStats = lstatSync(legacyPath);\n\tif (!legacyStats.isFile() || legacyStats.isSymbolicLink()) return;\n\tlet target = canonicalPath;\n\tif (existsSync(target)) {\n\t\ttarget = migrationConflictPath(agentDir, \"root-files\", legacyName.replaceAll(\":\", \".\")) ?? \"\";\n\t\tif (!target) return;\n\t}\n\tmkdirSync(dirname(target), { recursive: true });\n\ttry {\n\t\trenameSync(legacyPath, target);\n\t} catch (renameError) {\n\t\t// Windows cannot rename an NTFS alternate data stream into a regular file. Preserve the\n\t\t// bytes first, then remove only the named stream; never move or rewrite the owning auth file.\n\t\twriteFileSync(target, readFileSync(legacyPath), { flag: \"wx\" });\n\t\ttry {\n\t\t\tunlinkSync(legacyPath);\n\t\t} catch {\n\t\t\ttry {\n\t\t\t\tunlinkSync(target);\n\t\t\t} catch {}\n\t\t\tthrow renameError;\n\t\t}\n\t}\n}\n\n/** Remove only empty real per-project session directories; transcript files are never retention-pruned. */\nexport function pruneEmptySessionNamespaces(agentDir: string): string[] {\n\tconst root = sessionsDir(agentDir);\n\tlet candidates: string[];\n\ttry {\n\t\tcandidates = readdirSync(root, { withFileTypes: true })\n\t\t\t.slice(0, MAX_SESSION_NAMESPACES_TO_PRUNE)\n\t\t\t.filter((entry) => entry.isDirectory() && !entry.isSymbolicLink())\n\t\t\t.map((entry) => join(root, entry.name));\n\t} catch {\n\t\treturn [];\n\t}\n\n\tconst removed: string[] = [];\n\tfor (const candidate of candidates) {\n\t\ttry {\n\t\t\tconst stats = lstatSync(candidate);\n\t\t\tif (!stats.isDirectory() || stats.isSymbolicLink() || readdirSync(candidate).length > 0) continue;\n\t\t\trmdirSync(candidate);\n\t\t\tremoved.push(candidate);\n\t\t} catch {}\n\t}\n\treturn removed;\n}\n\n/**\n * Consolidate known machine-managed layout generations. Each migration is independently guarded:\n * startup never fails because cleanup is unavailable, and unknown files/resources remain untouched.\n */\nexport function migrateAgentDirLayout(agentDir: string): void {\n\ttry {\n\t\tmigrateTrustState(agentDir);\n\t} catch {\n\t\t// Best-effort: startup must not fail because one straggler could not be relocated.\n\t}\n\ttry {\n\t\tmigrateLegacyContextStores(agentDir);\n\t\tpruneContextStores(agentDir);\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"backups\", configBackupsDir(agentDir));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"resource-profiles\", directoryProfilesDir(agentDir));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"auto-learn\", stateFile(agentDir, \"legacy-layout\", \"auto-learn\"));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"tmp\", stateFile(agentDir, \"legacy-layout\", \"tmp\"));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentFile(\n\t\t\tagentDir,\n\t\t\t\"auth.json:Zone.Identifier\",\n\t\t\tstateFile(agentDir, \"legacy-layout\", \"sidecars\", \"auth.json.Zone.Identifier\"),\n\t\t);\n\t} catch {}\n\tpruneEmptySessionNamespaces(agentDir);\n}\n\n/**\n * Check for deprecated hooks/ and tools/ directories.\n * Note: tools/ may contain fd/rg binaries extracted by pi, so only warn if it has other files.\n */\nfunction checkDeprecatedExtensionDirs(baseDir: string, label: string): string[] {\n\tconst hooksDir = join(baseDir, \"hooks\");\n\tconst toolsDir = join(baseDir, \"tools\");\n\tconst warnings: string[] = [];\n\n\tif (existsSync(hooksDir)) {\n\t\twarnings.push(`${label} hooks/ directory found. Hooks have been renamed to extensions.`);\n\t}\n\n\tif (existsSync(toolsDir)) {\n\t\t// Check if tools/ contains anything other than fd/rg (which are auto-extracted binaries)\n\t\ttry {\n\t\t\tconst entries = readdirSync(toolsDir);\n\t\t\tconst customTools = entries.filter((e) => {\n\t\t\t\tconst lower = e.toLowerCase();\n\t\t\t\treturn (\n\t\t\t\t\tlower !== \"fd\" && lower !== \"rg\" && lower !== \"fd.exe\" && lower !== \"rg.exe\" && !e.startsWith(\".\") // Ignore .DS_Store and other hidden files\n\t\t\t\t);\n\t\t\t});\n\t\t\tif (customTools.length > 0) {\n\t\t\t\twarnings.push(\n\t\t\t\t\t`${label} tools/ directory contains custom tools. Custom tools have been merged into extensions.`,\n\t\t\t\t);\n\t\t\t}\n\t\t} catch {\n\t\t\t// Ignore read errors\n\t\t}\n\t}\n\n\treturn warnings;\n}\n\n/**\n * Run extension system migrations (commands→prompts) and collect warnings about deprecated directories.\n */\nfunction migrateExtensionSystem(cwd: string): string[] {\n\tconst agentDir = getAgentDir();\n\tconst projectDir = join(cwd, CONFIG_DIR_NAME);\n\n\t// Migrate commands/ to prompts/\n\tmigrateCommandsToPrompts(agentDir, \"Global\");\n\tmigrateCommandsToPrompts(projectDir, \"Project\");\n\n\t// Check for deprecated directories\n\tconst warnings = [\n\t\t...checkDeprecatedExtensionDirs(agentDir, \"Global\"),\n\t\t...checkDeprecatedExtensionDirs(projectDir, \"Project\"),\n\t];\n\n\treturn warnings;\n}\n\n/**\n * Print deprecation warnings and wait for keypress.\n */\nexport async function showDeprecationWarnings(warnings: string[]): Promise<void> {\n\tif (warnings.length === 0) return;\n\n\tfor (const warning of warnings) {\n\t\tconsole.log(chalk.yellow(`Warning: ${warning}`));\n\t}\n\tconsole.log(chalk.yellow(`\\nMove your extensions to the extensions/ directory.`));\n\tconsole.log(chalk.yellow(`Migration guide: ${MIGRATION_GUIDE_URL}`));\n\tconsole.log(chalk.yellow(`Documentation: ${EXTENSIONS_DOC_URL}`));\n\tif (!process.stdin.isTTY || !process.stdout.isTTY) {\n\t\tconsole.log();\n\t\treturn;\n\t}\n\tconsole.log(chalk.dim(`\\nPress any key to continue...`));\n\n\tawait new Promise<void>((resolve) => {\n\t\tlet settled = false;\n\t\tconst finish = () => {\n\t\t\tif (settled) return;\n\t\t\tsettled = true;\n\t\t\tprocess.stdin.removeListener(\"data\", finish);\n\t\t\tprocess.stdin.removeListener(\"end\", finish);\n\t\t\tprocess.stdin.removeListener(\"error\", finish);\n\t\t\tprocess.stdin.setRawMode?.(false);\n\t\t\tprocess.stdin.pause();\n\t\t\tresolve();\n\t\t};\n\t\tprocess.stdin.setRawMode?.(true);\n\t\tprocess.stdin.resume();\n\t\tprocess.stdin.once(\"data\", finish);\n\t\tprocess.stdin.once(\"end\", finish);\n\t\tprocess.stdin.once(\"error\", finish);\n\t});\n\tconsole.log();\n}\n\n/**\n * Run all migrations. Called once on startup.\n *\n * @returns Object with migration results and deprecation warnings\n */\nexport function runMigrations(cwd: string): {\n\tmigratedAuthProviders: string[];\n\tdeprecationWarnings: string[];\n} {\n\tmigrateAgentDirLayout(getAgentDir());\n\tconst migratedAuthProviders = migrateAuthToAuthJson();\n\tmigrateExplicitEnvVarConfigValues();\n\tmigrateSessionsFromAgentRoot();\n\tmigrateToolsToBin();\n\tmigrateKeybindingsConfigFile();\n\tconst deprecationWarnings = migrateExtensionSystem(cwd);\n\treturn { migratedAuthProviders, deprecationWarnings };\n}\n"]}

package/dist/migrations.js

@@ -2,11 +2,14 @@
  * One-time migrations that run on startup.
  */
 import chalk from "chalk";
-import { chmodSync, existsSync, mkdirSync, readdirSync, readFileSync, renameSync, rmSync, writeFileSync } from "fs";
+import { chmodSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, renameSync, rmdirSync, rmSync, unlinkSync, writeFileSync, } from "fs";
 import { dirname, join } from "path";
 import { CONFIG_DIR_NAME, getAgentDir, getBinDir } from "./config.js";
+import { configBackupsDir, directoryProfilesDir, sessionsDir, stateFile } from "./core/agent-paths.js";
+import { migrateLegacyContextStores, pruneContextStores } from "./core/context/context-store-retention.js";
 import { migrateKeybindingsConfig } from "./core/keybindings.js";
 import { isLegacyEnvVarNameConfigValue } from "./core/resolve-config-value.js";
+import { withFileLockSync, writeFileAtomicSync } from "./core/util/atomic-file.js";
 import { stripJsonComments } from "./utils/json.js";
 const MIGRATION_GUIDE_URL = "https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/CHANGELOG.md#extensions-migration";
 const EXTENSIONS_DOC_URL = "https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/docs/extensions.md";
@@ -323,6 +326,198 @@ function migrateToolsToBin() {
         console.log(chalk.green(`Migrated managed binaries tools/ → bin/`));
     }
 }
+/**
+ * Root-level machine-managed trust state is relocated into `state/`. If both layouts exist, valid
+ * entries are merged under the canonical file's lock and canonical decisions win conflicts.
+ */
+const MAX_SESSION_NAMESPACES_TO_PRUNE = 10_000;
+const MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE = 10_000;
+const MAX_MIGRATION_CONFLICT_SUFFIXES = 1_000;
+function readMigratedTrustFile(path) {
+    try {
+        const parsed = JSON.parse(readFileSync(path, "utf-8"));
+        if (typeof parsed !== "object" || parsed === null || Array.isArray(parsed))
+            return undefined;
+        const trust = {};
+        for (const [key, value] of Object.entries(parsed)) {
+            if (value !== true && value !== false && value !== null)
+                return undefined;
+            trust[key] = value;
+        }
+        return trust;
+    }
+    catch {
+        return undefined;
+    }
+}
+function migrateTrustState(agentDir) {
+    const oldPath = join(agentDir, "trust.json");
+    if (!existsSync(oldPath))
+        return;
+    const newPath = stateFile(agentDir, "trust.json");
+    if (!existsSync(newPath)) {
+        mkdirSync(dirname(newPath), { recursive: true });
+        renameSync(oldPath, newPath);
+        return;
+    }
+    withFileLockSync(newPath, () => {
+        const legacy = readMigratedTrustFile(oldPath);
+        const canonical = readMigratedTrustFile(newPath);
+        if (!legacy || !canonical)
+            return;
+        const merged = { ...legacy, ...canonical };
+        const sorted = Object.fromEntries(Object.entries(merged).sort(([left], [right]) => left.localeCompare(right)));
+        writeFileAtomicSync(newPath, `${JSON.stringify(sorted, null, 2)}\n`);
+        unlinkSync(oldPath);
+    });
+}
+function migrationConflictPath(agentDir, legacyName, entryName) {
+    const conflictDir = stateFile(agentDir, "migration-conflicts", legacyName);
+    for (let suffix = 0; suffix < MAX_MIGRATION_CONFLICT_SUFFIXES; suffix++) {
+        const name = suffix === 0 ? entryName : `${entryName}.legacy-${suffix}`;
+        const candidate = join(conflictDir, name);
+        if (!existsSync(candidate))
+            return candidate;
+    }
+    return undefined;
+}
+/**
+ * Relocate one known legacy root without traversing its contents. A whole-root rename is O(1);
+ * partial migrations scan a bounded number of top-level entries and preserve collisions under
+ * state/migration-conflicts instead of overwriting either copy.
+ */
+function migrateLegacyAgentDirectory(agentDir, legacyName, canonicalDir) {
+    const legacyDir = join(agentDir, legacyName);
+    if (!existsSync(legacyDir))
+        return;
+    const legacyStats = lstatSync(legacyDir);
+    if (!legacyStats.isDirectory() || legacyStats.isSymbolicLink())
+        return;
+    if (!existsSync(canonicalDir)) {
+        mkdirSync(dirname(canonicalDir), { recursive: true });
+        renameSync(legacyDir, canonicalDir);
+        return;
+    }
+    const canonicalStats = lstatSync(canonicalDir);
+    if (!canonicalStats.isDirectory() || canonicalStats.isSymbolicLink())
+        return;
+    const entries = readdirSync(legacyDir).slice(0, MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE);
+    for (const entry of entries) {
+        const source = join(legacyDir, entry);
+        let target = join(canonicalDir, entry);
+        if (existsSync(target)) {
+            target = migrationConflictPath(agentDir, legacyName, entry) ?? "";
+            if (!target)
+                continue;
+            mkdirSync(dirname(target), { recursive: true });
+        }
+        try {
+            renameSync(source, target);
+        }
+        catch { }
+    }
+    try {
+        rmdirSync(legacyDir);
+    }
+    catch { }
+}
+function migrateLegacyAgentFile(agentDir, legacyName, canonicalPath) {
+    const legacyPath = join(agentDir, legacyName);
+    if (!existsSync(legacyPath))
+        return;
+    const legacyStats = lstatSync(legacyPath);
+    if (!legacyStats.isFile() || legacyStats.isSymbolicLink())
+        return;
+    let target = canonicalPath;
+    if (existsSync(target)) {
+        target = migrationConflictPath(agentDir, "root-files", legacyName.replaceAll(":", ".")) ?? "";
+        if (!target)
+            return;
+    }
+    mkdirSync(dirname(target), { recursive: true });
+    try {
+        renameSync(legacyPath, target);
+    }
+    catch (renameError) {
+        // Windows cannot rename an NTFS alternate data stream into a regular file. Preserve the
+        // bytes first, then remove only the named stream; never move or rewrite the owning auth file.
+        writeFileSync(target, readFileSync(legacyPath), { flag: "wx" });
+        try {
+            unlinkSync(legacyPath);
+        }
+        catch {
+            try {
+                unlinkSync(target);
+            }
+            catch { }
+            throw renameError;
+        }
+    }
+}
+/** Remove only empty real per-project session directories; transcript files are never retention-pruned. */
+export function pruneEmptySessionNamespaces(agentDir) {
+    const root = sessionsDir(agentDir);
+    let candidates;
+    try {
+        candidates = readdirSync(root, { withFileTypes: true })
+            .slice(0, MAX_SESSION_NAMESPACES_TO_PRUNE)
+            .filter((entry) => entry.isDirectory() && !entry.isSymbolicLink())
+            .map((entry) => join(root, entry.name));
+    }
+    catch {
+        return [];
+    }
+    const removed = [];
+    for (const candidate of candidates) {
+        try {
+            const stats = lstatSync(candidate);
+            if (!stats.isDirectory() || stats.isSymbolicLink() || readdirSync(candidate).length > 0)
+                continue;
+            rmdirSync(candidate);
+            removed.push(candidate);
+        }
+        catch { }
+    }
+    return removed;
+}
+/**
+ * Consolidate known machine-managed layout generations. Each migration is independently guarded:
+ * startup never fails because cleanup is unavailable, and unknown files/resources remain untouched.
+ */
+export function migrateAgentDirLayout(agentDir) {
+    try {
+        migrateTrustState(agentDir);
+    }
+    catch {
+        // Best-effort: startup must not fail because one straggler could not be relocated.
+    }
+    try {
+        migrateLegacyContextStores(agentDir);
+        pruneContextStores(agentDir);
+    }
+    catch { }
+    try {
+        migrateLegacyAgentDirectory(agentDir, "backups", configBackupsDir(agentDir));
+    }
+    catch { }
+    try {
+        migrateLegacyAgentDirectory(agentDir, "resource-profiles", directoryProfilesDir(agentDir));
+    }
+    catch { }
+    try {
+        migrateLegacyAgentDirectory(agentDir, "auto-learn", stateFile(agentDir, "legacy-layout", "auto-learn"));
+    }
+    catch { }
+    try {
+        migrateLegacyAgentDirectory(agentDir, "tmp", stateFile(agentDir, "legacy-layout", "tmp"));
+    }
+    catch { }
+    try {
+        migrateLegacyAgentFile(agentDir, "auth.json:Zone.Identifier", stateFile(agentDir, "legacy-layout", "sidecars", "auth.json.Zone.Identifier"));
+    }
+    catch { }
+    pruneEmptySessionNamespaces(agentDir);
+}
 /**
  * Check for deprecated hooks/ and tools/ directories.
  * Note: tools/ may contain fd/rg binaries extracted by pi, so only warn if it has other files.
@@ -413,6 +608,7 @@ export async function showDeprecationWarnings(warnings) {
  * @returns Object with migration results and deprecation warnings
  */
 export function runMigrations(cwd) {
+    migrateAgentDirLayout(getAgentDir());
     const migratedAuthProviders = migrateAuthToAuthJson();
     migrateExplicitEnvVarConfigValues();
     migrateSessionsFromAgentRoot();

package/dist/migrations.js.map

@@ -1 +1 @@
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* One-time migrations that run on startup.\n */\n\nimport chalk from \"chalk\";\nimport { chmodSync, existsSync, mkdirSync, readdirSync, readFileSync, renameSync, rmSync, writeFileSync } from \"fs\";\nimport { dirname, join } from \"path\";\nimport { CONFIG_DIR_NAME, getAgentDir, getBinDir } from \"./config.ts\";\nimport { migrateKeybindingsConfig } from \"./core/keybindings.ts\";\nimport { isLegacyEnvVarNameConfigValue } from \"./core/resolve-config-value.ts\";\nimport { stripJsonComments } from \"./utils/json.ts\";\n\nconst MIGRATION_GUIDE_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/CHANGELOG.md#extensions-migration\";\nconst EXTENSIONS_DOC_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/docs/extensions.md\";\n\n/**\n * Migrate legacy oauth.json and settings.json apiKeys to auth.json.\n *\n * @returns Array of provider names that were migrated\n */\nexport function migrateAuthToAuthJson(): string[] {\n\tconst agentDir = getAgentDir();\n\tconst authPath = join(agentDir, \"auth.json\");\n\tconst oauthPath = join(agentDir, \"oauth.json\");\n\tconst settingsPath = join(agentDir, \"settings.json\");\n\n\t// Skip if auth.json already exists\n\tif (existsSync(authPath)) return [];\n\n\tconst migrated: Record<string, unknown> = {};\n\tconst providers: string[] = [];\n\n\t// Migrate oauth.json\n\tif (existsSync(oauthPath)) {\n\t\ttry {\n\t\t\tconst oauth = JSON.parse(readFileSync(oauthPath, \"utf-8\"));\n\t\t\tfor (const [provider, cred] of Object.entries(oauth)) {\n\t\t\t\tmigrated[provider] = { type: \"oauth\", ...(cred as object) };\n\t\t\t\tproviders.push(provider);\n\t\t\t}\n\t\t\trenameSync(oauthPath, `${oauthPath}.migrated`);\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\t// Migrate settings.json apiKeys\n\tif (existsSync(settingsPath)) {\n\t\ttry {\n\t\t\tconst content = readFileSync(settingsPath, \"utf-8\");\n\t\t\tconst settings = JSON.parse(content);\n\t\t\tif (settings.apiKeys && typeof settings.apiKeys === \"object\") {\n\t\t\t\tfor (const [provider, key] of Object.entries(settings.apiKeys)) {\n\t\t\t\t\tif (!migrated[provider] && typeof key === \"string\") {\n\t\t\t\t\t\tmigrated[provider] = { type: \"api_key\", key };\n\t\t\t\t\t\tproviders.push(provider);\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tdelete settings.apiKeys;\n\t\t\t\twriteFileSync(settingsPath, JSON.stringify(settings, null, 2));\n\t\t\t}\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\tif (Object.keys(migrated).length > 0) {\n\t\tmkdirSync(dirname(authPath), { recursive: true });\n\t\twriteFileSync(authPath, JSON.stringify(migrated, null, 2), { mode: 0o600 });\n\t}\n\n\treturn providers;\n}\n\ninterface ConfigValueMigration {\n\tlocation: string;\n\tfrom: string;\n\tto: string;\n}\n\nfunction migrateLegacyEnvVarString(value: string): string | undefined {\n\treturn isLegacyEnvVarNameConfigValue(value) ? `$${value}` : undefined;\n}\n\nfunction migrateStringProperty(\n\trecord: Record<string, unknown>,\n\tkey: string,\n\tlocation: string,\n\tmigrations: ConfigValueMigration[],\n): boolean {\n\tconst value = record[key];\n\tif (typeof value !== \"string\") return false;\n\tconst migrated = migrateLegacyEnvVarString(value);\n\tif (migrated === undefined) return false;\n\trecord[key] = migrated;\n\tmigrations.push({ location, from: value, to: migrated });\n\treturn true;\n}\n\nfunction migrateHeadersConfig(headers: unknown, location: string, migrations: ConfigValueMigration[]): boolean {\n\tif (typeof headers !== \"object\" || headers === null || Array.isArray(headers)) return false;\n\tconst headerRecord = headers as Record<string, unknown>;\n\tlet migrated = false;\n\tfor (const [key, value] of Object.entries(headerRecord)) {\n\t\tif (typeof value !== \"string\") continue;\n\t\tconst migratedValue = migrateLegacyEnvVarString(value);\n\t\tif (migratedValue === undefined) continue;\n\t\theaderRecord[key] = migratedValue;\n\t\tmigrations.push({ location: `${location}[${JSON.stringify(key)}]`, from: value, to: migratedValue });\n\t\tmigrated = true;\n\t}\n\treturn migrated;\n}\n\nfunction migrateAuthJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst authPath = join(agentDir, \"auth.json\");\n\tif (!existsSync(authPath)) return [];\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(authPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\t\tconst authData = parsed as Record<string, unknown>;\n\n\t\tconst migrations: ConfigValueMigration[] = [];\n\t\tfor (const [provider, credential] of Object.entries(authData)) {\n\t\t\tif (typeof credential !== \"object\" || credential === null || Array.isArray(credential)) continue;\n\t\t\tconst credentialRecord = credential as Record<string, unknown>;\n\t\t\tif (credentialRecord.type !== \"api_key\") continue;\n\t\t\tmigrateStringProperty(credentialRecord, \"key\", `auth.json[${JSON.stringify(provider)}].key`, migrations);\n\t\t}\n\n\t\tif (migrations.length === 0) return [];\n\t\twriteFileSync(authPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\t\tchmodSync(authPath, 0o600);\n\t\treturn migrations;\n\t} catch {\n\t\treturn [];\n\t}\n}\n\nfunction migrateModelsJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst modelsPath = join(agentDir, \"models.json\");\n\tif (!existsSync(modelsPath)) return [];\n\n\tlet parsed: unknown;\n\ttry {\n\t\tparsed = JSON.parse(stripJsonComments(readFileSync(modelsPath, \"utf-8\"))) as unknown;\n\t} catch {\n\t\treturn [];\n\t}\n\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\tconst modelsData = parsed as Record<string, unknown>;\n\tconst providers = modelsData.providers;\n\tif (typeof providers !== \"object\" || providers === null || Array.isArray(providers)) return [];\n\n\tconst migrations: ConfigValueMigration[] = [];\n\tfor (const [provider, providerConfig] of Object.entries(providers)) {\n\t\tif (typeof providerConfig !== \"object\" || providerConfig === null || Array.isArray(providerConfig)) continue;\n\t\tconst providerRecord = providerConfig as Record<string, unknown>;\n\t\tconst providerLocation = `models.json.providers[${JSON.stringify(provider)}]`;\n\t\tmigrateStringProperty(providerRecord, \"apiKey\", `${providerLocation}.apiKey`, migrations);\n\t\tmigrateHeadersConfig(providerRecord.headers, `${providerLocation}.headers`, migrations);\n\n\t\tif (Array.isArray(providerRecord.models)) {\n\t\t\tfor (let index = 0; index < providerRecord.models.length; index++) {\n\t\t\t\tconst modelConfig = providerRecord.models[index];\n\t\t\t\tif (typeof modelConfig !== \"object\" || modelConfig === null || Array.isArray(modelConfig)) continue;\n\t\t\t\tconst modelRecord = modelConfig as Record<string, unknown>;\n\t\t\t\tconst modelKey = typeof modelRecord.id === \"string\" ? JSON.stringify(modelRecord.id) : String(index);\n\t\t\t\tmigrateHeadersConfig(modelRecord.headers, `${providerLocation}.models[${modelKey}].headers`, migrations);\n\t\t\t}\n\t\t}\n\n\t\tconst modelOverrides = providerRecord.modelOverrides;\n\t\tif (typeof modelOverrides === \"object\" && modelOverrides !== null && !Array.isArray(modelOverrides)) {\n\t\t\tfor (const [modelId, modelOverride] of Object.entries(modelOverrides)) {\n\t\t\t\tif (typeof modelOverride !== \"object\" || modelOverride === null || Array.isArray(modelOverride)) continue;\n\t\t\t\tconst modelOverrideRecord = modelOverride as Record<string, unknown>;\n\t\t\t\tmigrateHeadersConfig(\n\t\t\t\t\tmodelOverrideRecord.headers,\n\t\t\t\t\t`${providerLocation}.modelOverrides[${JSON.stringify(modelId)}].headers`,\n\t\t\t\t\tmigrations,\n\t\t\t\t);\n\t\t\t}\n\t\t}\n\t}\n\n\tif (migrations.length === 0) return [];\n\twriteFileSync(modelsPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\treturn migrations;\n}\n\nfunction migrateExplicitEnvVarConfigValues(): void {\n\tconst agentDir = getAgentDir();\n\tconst migrations = [...migrateAuthJsonConfigValues(agentDir), ...migrateModelsJsonConfigValues(agentDir)];\n\tif (migrations.length === 0) return;\n\n\tconst details = migrations.map((migration) => `  - ${migration.location}: ${migration.from} -> ${migration.to}`);\n\tconsole.log(\n\t\tchalk.yellow(\n\t\t\t[\n\t\t\t\t\"Warning: Migrated API key/header environment references to explicit $ENV_VAR syntax. Plain strings will be treated as literals.\",\n\t\t\t\t...details,\n\t\t\t].join(\"\\n\"),\n\t\t),\n\t);\n}\n\n/**\n * Migrate sessions from ~/.pi/agent/*.jsonl to proper session directories.\n *\n * Bug in v0.30.0: Sessions were saved to ~/.pi/agent/ instead of\n * ~/.pi/agent/sessions/<encoded-cwd>/. This migration moves them\n * to the correct location based on the cwd in their session header.\n *\n * See: https://github.com/earendil-works/pi-mono/issues/320\n */\nexport function getMigratedSessionFileName(file: string): string | undefined {\n\tconst fileName = file.split(/[\\\\/]/).pop();\n\treturn fileName || undefined;\n}\n\nexport function migrateSessionsFromAgentRoot(): void {\n\tconst agentDir = getAgentDir();\n\n\t// Find all .jsonl files directly in agentDir (not in subdirectories)\n\tlet files: string[];\n\ttry {\n\t\tfiles = readdirSync(agentDir)\n\t\t\t.filter((f) => f.endsWith(\".jsonl\"))\n\t\t\t.map((f) => join(agentDir, f));\n\t} catch {\n\t\treturn;\n\t}\n\n\tif (files.length === 0) return;\n\n\tfor (const file of files) {\n\t\ttry {\n\t\t\t// Read first line to get session header\n\t\t\tconst content = readFileSync(file, \"utf8\");\n\t\t\tconst firstLine = content.split(\"\\n\")[0];\n\t\t\tif (!firstLine?.trim()) continue;\n\n\t\t\tconst header = JSON.parse(firstLine);\n\t\t\tif (header.type !== \"session\" || !header.cwd) continue;\n\n\t\t\tconst cwd: string = header.cwd;\n\n\t\t\t// Compute the correct session directory (same encoding as session-manager.ts)\n\t\t\tconst safePath = `--${cwd.replace(/^[/\\\\]/, \"\").replace(/[/\\\\:]/g, \"-\")}--`;\n\t\t\tconst correctDir = join(agentDir, \"sessions\", safePath);\n\n\t\t\t// Create directory if needed\n\t\t\tif (!existsSync(correctDir)) {\n\t\t\t\tmkdirSync(correctDir, { recursive: true });\n\t\t\t}\n\n\t\t\t// Move the file\n\t\t\tconst fileName = getMigratedSessionFileName(file);\n\t\t\tif (!fileName) continue;\n\t\t\tconst newPath = join(correctDir, fileName);\n\n\t\t\tif (existsSync(newPath)) continue; // Skip if target exists\n\n\t\t\trenameSync(file, newPath);\n\t\t} catch {\n\t\t\t// Skip files that can't be migrated\n\t\t}\n\t}\n}\n\n/**\n * Migrate commands/ to prompts/ if needed.\n * Works for both regular directories and symlinks.\n */\nfunction migrateCommandsToPrompts(baseDir: string, label: string): boolean {\n\tconst commandsDir = join(baseDir, \"commands\");\n\tconst promptsDir = join(baseDir, \"prompts\");\n\n\tif (existsSync(commandsDir) && !existsSync(promptsDir)) {\n\t\ttry {\n\t\t\trenameSync(commandsDir, promptsDir);\n\t\t\tconsole.log(chalk.green(`Migrated ${label} commands/ → prompts/`));\n\t\t\treturn true;\n\t\t} catch (err) {\n\t\t\tconsole.log(\n\t\t\t\tchalk.yellow(\n\t\t\t\t\t`Warning: Could not migrate ${label} commands/ to prompts/: ${err instanceof Error ? err.message : err}`,\n\t\t\t\t),\n\t\t\t);\n\t\t}\n\t}\n\treturn false;\n}\n\nfunction migrateKeybindingsConfigFile(): void {\n\tconst configPath = join(getAgentDir(), \"keybindings.json\");\n\tif (!existsSync(configPath)) return;\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(configPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) {\n\t\t\treturn;\n\t\t}\n\t\tconst { config, migrated } = migrateKeybindingsConfig(parsed as Record<string, unknown>);\n\t\tif (!migrated) return;\n\t\twriteFileSync(configPath, `${JSON.stringify(config, null, 2)}\\n`, \"utf-8\");\n\t} catch {\n\t\t// Ignore malformed files during migration\n\t}\n}\n\n/**\n * Move fd/rg binaries from tools/ to bin/ if they exist.\n */\nfunction migrateToolsToBin(): void {\n\tconst agentDir = getAgentDir();\n\tconst toolsDir = join(agentDir, \"tools\");\n\tconst binDir = getBinDir();\n\n\tif (!existsSync(toolsDir)) return;\n\n\tconst binaries = [\"fd\", \"rg\", \"fd.exe\", \"rg.exe\"];\n\tlet movedAny = false;\n\n\tfor (const bin of binaries) {\n\t\tconst oldPath = join(toolsDir, bin);\n\t\tconst newPath = join(binDir, bin);\n\n\t\tif (existsSync(oldPath)) {\n\t\t\tif (!existsSync(binDir)) {\n\t\t\t\tmkdirSync(binDir, { recursive: true });\n\t\t\t}\n\t\t\tif (!existsSync(newPath)) {\n\t\t\t\ttry {\n\t\t\t\t\trenameSync(oldPath, newPath);\n\t\t\t\t\tmovedAny = true;\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore errors\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// Target exists, just delete the old one\n\t\t\t\ttry {\n\t\t\t\t\trmSync?.(oldPath, { force: true });\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tif (movedAny) {\n\t\tconsole.log(chalk.green(`Migrated managed binaries tools/ → bin/`));\n\t}\n}\n\n/**\n * Check for deprecated hooks/ and tools/ directories.\n * Note: tools/ may contain fd/rg binaries extracted by pi, so only warn if it has other files.\n */\nfunction checkDeprecatedExtensionDirs(baseDir: string, label: string): string[] {\n\tconst hooksDir = join(baseDir, \"hooks\");\n\tconst toolsDir = join(baseDir, \"tools\");\n\tconst warnings: string[] = [];\n\n\tif (existsSync(hooksDir)) {\n\t\twarnings.push(`${label} hooks/ directory found. Hooks have been renamed to extensions.`);\n\t}\n\n\tif (existsSync(toolsDir)) {\n\t\t// Check if tools/ contains anything other than fd/rg (which are auto-extracted binaries)\n\t\ttry {\n\t\t\tconst entries = readdirSync(toolsDir);\n\t\t\tconst customTools = entries.filter((e) => {\n\t\t\t\tconst lower = e.toLowerCase();\n\t\t\t\treturn (\n\t\t\t\t\tlower !== \"fd\" && lower !== \"rg\" && lower !== \"fd.exe\" && lower !== \"rg.exe\" && !e.startsWith(\".\") // Ignore .DS_Store and other hidden files\n\t\t\t\t);\n\t\t\t});\n\t\t\tif (customTools.length > 0) {\n\t\t\t\twarnings.push(\n\t\t\t\t\t`${label} tools/ directory contains custom tools. Custom tools have been merged into extensions.`,\n\t\t\t\t);\n\t\t\t}\n\t\t} catch {\n\t\t\t// Ignore read errors\n\t\t}\n\t}\n\n\treturn warnings;\n}\n\n/**\n * Run extension system migrations (commands→prompts) and collect warnings about deprecated directories.\n */\nfunction migrateExtensionSystem(cwd: string): string[] {\n\tconst agentDir = getAgentDir();\n\tconst projectDir = join(cwd, CONFIG_DIR_NAME);\n\n\t// Migrate commands/ to prompts/\n\tmigrateCommandsToPrompts(agentDir, \"Global\");\n\tmigrateCommandsToPrompts(projectDir, \"Project\");\n\n\t// Check for deprecated directories\n\tconst warnings = [\n\t\t...checkDeprecatedExtensionDirs(agentDir, \"Global\"),\n\t\t...checkDeprecatedExtensionDirs(projectDir, \"Project\"),\n\t];\n\n\treturn warnings;\n}\n\n/**\n * Print deprecation warnings and wait for keypress.\n */\nexport async function showDeprecationWarnings(warnings: string[]): Promise<void> {\n\tif (warnings.length === 0) return;\n\n\tfor (const warning of warnings) {\n\t\tconsole.log(chalk.yellow(`Warning: ${warning}`));\n\t}\n\tconsole.log(chalk.yellow(`\\nMove your extensions to the extensions/ directory.`));\n\tconsole.log(chalk.yellow(`Migration guide: ${MIGRATION_GUIDE_URL}`));\n\tconsole.log(chalk.yellow(`Documentation: ${EXTENSIONS_DOC_URL}`));\n\tif (!process.stdin.isTTY || !process.stdout.isTTY) {\n\t\tconsole.log();\n\t\treturn;\n\t}\n\tconsole.log(chalk.dim(`\\nPress any key to continue...`));\n\n\tawait new Promise<void>((resolve) => {\n\t\tlet settled = false;\n\t\tconst finish = () => {\n\t\t\tif (settled) return;\n\t\t\tsettled = true;\n\t\t\tprocess.stdin.removeListener(\"data\", finish);\n\t\t\tprocess.stdin.removeListener(\"end\", finish);\n\t\t\tprocess.stdin.removeListener(\"error\", finish);\n\t\t\tprocess.stdin.setRawMode?.(false);\n\t\t\tprocess.stdin.pause();\n\t\t\tresolve();\n\t\t};\n\t\tprocess.stdin.setRawMode?.(true);\n\t\tprocess.stdin.resume();\n\t\tprocess.stdin.once(\"data\", finish);\n\t\tprocess.stdin.once(\"end\", finish);\n\t\tprocess.stdin.once(\"error\", finish);\n\t});\n\tconsole.log();\n}\n\n/**\n * Run all migrations. Called once on startup.\n *\n * @returns Object with migration results and deprecation warnings\n */\nexport function runMigrations(cwd: string): {\n\tmigratedAuthProviders: string[];\n\tdeprecationWarnings: string[];\n} {\n\tconst migratedAuthProviders = migrateAuthToAuthJson();\n\tmigrateExplicitEnvVarConfigValues();\n\tmigrateSessionsFromAgentRoot();\n\tmigrateToolsToBin();\n\tmigrateKeybindingsConfigFile();\n\tconst deprecationWarnings = migrateExtensionSystem(cwd);\n\treturn { migratedAuthProviders, deprecationWarnings };\n}\n"]}
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* One-time migrations that run on startup.\n */\n\nimport chalk from \"chalk\";\nimport {\n\tchmodSync,\n\texistsSync,\n\tlstatSync,\n\tmkdirSync,\n\treaddirSync,\n\treadFileSync,\n\trenameSync,\n\trmdirSync,\n\trmSync,\n\tunlinkSync,\n\twriteFileSync,\n} from \"fs\";\nimport { dirname, join } from \"path\";\nimport { CONFIG_DIR_NAME, getAgentDir, getBinDir } from \"./config.ts\";\nimport { configBackupsDir, directoryProfilesDir, sessionsDir, stateFile } from \"./core/agent-paths.ts\";\nimport { migrateLegacyContextStores, pruneContextStores } from \"./core/context/context-store-retention.ts\";\nimport { migrateKeybindingsConfig } from \"./core/keybindings.ts\";\nimport { isLegacyEnvVarNameConfigValue } from \"./core/resolve-config-value.ts\";\nimport { withFileLockSync, writeFileAtomicSync } from \"./core/util/atomic-file.ts\";\nimport { stripJsonComments } from \"./utils/json.ts\";\n\nconst MIGRATION_GUIDE_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/CHANGELOG.md#extensions-migration\";\nconst EXTENSIONS_DOC_URL =\n\t\"https://github.com/earendil-works/pi-mono/blob/main/packages/coding-agent/docs/extensions.md\";\n\n/**\n * Migrate legacy oauth.json and settings.json apiKeys to auth.json.\n *\n * @returns Array of provider names that were migrated\n */\nexport function migrateAuthToAuthJson(): string[] {\n\tconst agentDir = getAgentDir();\n\tconst authPath = join(agentDir, \"auth.json\");\n\tconst oauthPath = join(agentDir, \"oauth.json\");\n\tconst settingsPath = join(agentDir, \"settings.json\");\n\n\t// Skip if auth.json already exists\n\tif (existsSync(authPath)) return [];\n\n\tconst migrated: Record<string, unknown> = {};\n\tconst providers: string[] = [];\n\n\t// Migrate oauth.json\n\tif (existsSync(oauthPath)) {\n\t\ttry {\n\t\t\tconst oauth = JSON.parse(readFileSync(oauthPath, \"utf-8\"));\n\t\t\tfor (const [provider, cred] of Object.entries(oauth)) {\n\t\t\t\tmigrated[provider] = { type: \"oauth\", ...(cred as object) };\n\t\t\t\tproviders.push(provider);\n\t\t\t}\n\t\t\trenameSync(oauthPath, `${oauthPath}.migrated`);\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\t// Migrate settings.json apiKeys\n\tif (existsSync(settingsPath)) {\n\t\ttry {\n\t\t\tconst content = readFileSync(settingsPath, \"utf-8\");\n\t\t\tconst settings = JSON.parse(content);\n\t\t\tif (settings.apiKeys && typeof settings.apiKeys === \"object\") {\n\t\t\t\tfor (const [provider, key] of Object.entries(settings.apiKeys)) {\n\t\t\t\t\tif (!migrated[provider] && typeof key === \"string\") {\n\t\t\t\t\t\tmigrated[provider] = { type: \"api_key\", key };\n\t\t\t\t\t\tproviders.push(provider);\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tdelete settings.apiKeys;\n\t\t\t\twriteFileSync(settingsPath, JSON.stringify(settings, null, 2));\n\t\t\t}\n\t\t} catch {\n\t\t\t// Skip on error\n\t\t}\n\t}\n\n\tif (Object.keys(migrated).length > 0) {\n\t\tmkdirSync(dirname(authPath), { recursive: true });\n\t\twriteFileSync(authPath, JSON.stringify(migrated, null, 2), { mode: 0o600 });\n\t}\n\n\treturn providers;\n}\n\ninterface ConfigValueMigration {\n\tlocation: string;\n\tfrom: string;\n\tto: string;\n}\n\nfunction migrateLegacyEnvVarString(value: string): string | undefined {\n\treturn isLegacyEnvVarNameConfigValue(value) ? `$${value}` : undefined;\n}\n\nfunction migrateStringProperty(\n\trecord: Record<string, unknown>,\n\tkey: string,\n\tlocation: string,\n\tmigrations: ConfigValueMigration[],\n): boolean {\n\tconst value = record[key];\n\tif (typeof value !== \"string\") return false;\n\tconst migrated = migrateLegacyEnvVarString(value);\n\tif (migrated === undefined) return false;\n\trecord[key] = migrated;\n\tmigrations.push({ location, from: value, to: migrated });\n\treturn true;\n}\n\nfunction migrateHeadersConfig(headers: unknown, location: string, migrations: ConfigValueMigration[]): boolean {\n\tif (typeof headers !== \"object\" || headers === null || Array.isArray(headers)) return false;\n\tconst headerRecord = headers as Record<string, unknown>;\n\tlet migrated = false;\n\tfor (const [key, value] of Object.entries(headerRecord)) {\n\t\tif (typeof value !== \"string\") continue;\n\t\tconst migratedValue = migrateLegacyEnvVarString(value);\n\t\tif (migratedValue === undefined) continue;\n\t\theaderRecord[key] = migratedValue;\n\t\tmigrations.push({ location: `${location}[${JSON.stringify(key)}]`, from: value, to: migratedValue });\n\t\tmigrated = true;\n\t}\n\treturn migrated;\n}\n\nfunction migrateAuthJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst authPath = join(agentDir, \"auth.json\");\n\tif (!existsSync(authPath)) return [];\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(authPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\t\tconst authData = parsed as Record<string, unknown>;\n\n\t\tconst migrations: ConfigValueMigration[] = [];\n\t\tfor (const [provider, credential] of Object.entries(authData)) {\n\t\t\tif (typeof credential !== \"object\" || credential === null || Array.isArray(credential)) continue;\n\t\t\tconst credentialRecord = credential as Record<string, unknown>;\n\t\t\tif (credentialRecord.type !== \"api_key\") continue;\n\t\t\tmigrateStringProperty(credentialRecord, \"key\", `auth.json[${JSON.stringify(provider)}].key`, migrations);\n\t\t}\n\n\t\tif (migrations.length === 0) return [];\n\t\twriteFileSync(authPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\t\tchmodSync(authPath, 0o600);\n\t\treturn migrations;\n\t} catch {\n\t\treturn [];\n\t}\n}\n\nfunction migrateModelsJsonConfigValues(agentDir: string): ConfigValueMigration[] {\n\tconst modelsPath = join(agentDir, \"models.json\");\n\tif (!existsSync(modelsPath)) return [];\n\n\tlet parsed: unknown;\n\ttry {\n\t\tparsed = JSON.parse(stripJsonComments(readFileSync(modelsPath, \"utf-8\"))) as unknown;\n\t} catch {\n\t\treturn [];\n\t}\n\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return [];\n\tconst modelsData = parsed as Record<string, unknown>;\n\tconst providers = modelsData.providers;\n\tif (typeof providers !== \"object\" || providers === null || Array.isArray(providers)) return [];\n\n\tconst migrations: ConfigValueMigration[] = [];\n\tfor (const [provider, providerConfig] of Object.entries(providers)) {\n\t\tif (typeof providerConfig !== \"object\" || providerConfig === null || Array.isArray(providerConfig)) continue;\n\t\tconst providerRecord = providerConfig as Record<string, unknown>;\n\t\tconst providerLocation = `models.json.providers[${JSON.stringify(provider)}]`;\n\t\tmigrateStringProperty(providerRecord, \"apiKey\", `${providerLocation}.apiKey`, migrations);\n\t\tmigrateHeadersConfig(providerRecord.headers, `${providerLocation}.headers`, migrations);\n\n\t\tif (Array.isArray(providerRecord.models)) {\n\t\t\tfor (let index = 0; index < providerRecord.models.length; index++) {\n\t\t\t\tconst modelConfig = providerRecord.models[index];\n\t\t\t\tif (typeof modelConfig !== \"object\" || modelConfig === null || Array.isArray(modelConfig)) continue;\n\t\t\t\tconst modelRecord = modelConfig as Record<string, unknown>;\n\t\t\t\tconst modelKey = typeof modelRecord.id === \"string\" ? JSON.stringify(modelRecord.id) : String(index);\n\t\t\t\tmigrateHeadersConfig(modelRecord.headers, `${providerLocation}.models[${modelKey}].headers`, migrations);\n\t\t\t}\n\t\t}\n\n\t\tconst modelOverrides = providerRecord.modelOverrides;\n\t\tif (typeof modelOverrides === \"object\" && modelOverrides !== null && !Array.isArray(modelOverrides)) {\n\t\t\tfor (const [modelId, modelOverride] of Object.entries(modelOverrides)) {\n\t\t\t\tif (typeof modelOverride !== \"object\" || modelOverride === null || Array.isArray(modelOverride)) continue;\n\t\t\t\tconst modelOverrideRecord = modelOverride as Record<string, unknown>;\n\t\t\t\tmigrateHeadersConfig(\n\t\t\t\t\tmodelOverrideRecord.headers,\n\t\t\t\t\t`${providerLocation}.modelOverrides[${JSON.stringify(modelId)}].headers`,\n\t\t\t\t\tmigrations,\n\t\t\t\t);\n\t\t\t}\n\t\t}\n\t}\n\n\tif (migrations.length === 0) return [];\n\twriteFileSync(modelsPath, `${JSON.stringify(parsed, null, 2)}\\n`, \"utf-8\");\n\treturn migrations;\n}\n\nfunction migrateExplicitEnvVarConfigValues(): void {\n\tconst agentDir = getAgentDir();\n\tconst migrations = [...migrateAuthJsonConfigValues(agentDir), ...migrateModelsJsonConfigValues(agentDir)];\n\tif (migrations.length === 0) return;\n\n\tconst details = migrations.map((migration) => `  - ${migration.location}: ${migration.from} -> ${migration.to}`);\n\tconsole.log(\n\t\tchalk.yellow(\n\t\t\t[\n\t\t\t\t\"Warning: Migrated API key/header environment references to explicit $ENV_VAR syntax. Plain strings will be treated as literals.\",\n\t\t\t\t...details,\n\t\t\t].join(\"\\n\"),\n\t\t),\n\t);\n}\n\n/**\n * Migrate sessions from ~/.pi/agent/*.jsonl to proper session directories.\n *\n * Bug in v0.30.0: Sessions were saved to ~/.pi/agent/ instead of\n * ~/.pi/agent/sessions/<encoded-cwd>/. This migration moves them\n * to the correct location based on the cwd in their session header.\n *\n * See: https://github.com/earendil-works/pi-mono/issues/320\n */\nexport function getMigratedSessionFileName(file: string): string | undefined {\n\tconst fileName = file.split(/[\\\\/]/).pop();\n\treturn fileName || undefined;\n}\n\nexport function migrateSessionsFromAgentRoot(): void {\n\tconst agentDir = getAgentDir();\n\n\t// Find all .jsonl files directly in agentDir (not in subdirectories)\n\tlet files: string[];\n\ttry {\n\t\tfiles = readdirSync(agentDir)\n\t\t\t.filter((f) => f.endsWith(\".jsonl\"))\n\t\t\t.map((f) => join(agentDir, f));\n\t} catch {\n\t\treturn;\n\t}\n\n\tif (files.length === 0) return;\n\n\tfor (const file of files) {\n\t\ttry {\n\t\t\t// Read first line to get session header\n\t\t\tconst content = readFileSync(file, \"utf8\");\n\t\t\tconst firstLine = content.split(\"\\n\")[0];\n\t\t\tif (!firstLine?.trim()) continue;\n\n\t\t\tconst header = JSON.parse(firstLine);\n\t\t\tif (header.type !== \"session\" || !header.cwd) continue;\n\n\t\t\tconst cwd: string = header.cwd;\n\n\t\t\t// Compute the correct session directory (same encoding as session-manager.ts)\n\t\t\tconst safePath = `--${cwd.replace(/^[/\\\\]/, \"\").replace(/[/\\\\:]/g, \"-\")}--`;\n\t\t\tconst correctDir = join(agentDir, \"sessions\", safePath);\n\n\t\t\t// Create directory if needed\n\t\t\tif (!existsSync(correctDir)) {\n\t\t\t\tmkdirSync(correctDir, { recursive: true });\n\t\t\t}\n\n\t\t\t// Move the file\n\t\t\tconst fileName = getMigratedSessionFileName(file);\n\t\t\tif (!fileName) continue;\n\t\t\tconst newPath = join(correctDir, fileName);\n\n\t\t\tif (existsSync(newPath)) continue; // Skip if target exists\n\n\t\t\trenameSync(file, newPath);\n\t\t} catch {\n\t\t\t// Skip files that can't be migrated\n\t\t}\n\t}\n}\n\n/**\n * Migrate commands/ to prompts/ if needed.\n * Works for both regular directories and symlinks.\n */\nfunction migrateCommandsToPrompts(baseDir: string, label: string): boolean {\n\tconst commandsDir = join(baseDir, \"commands\");\n\tconst promptsDir = join(baseDir, \"prompts\");\n\n\tif (existsSync(commandsDir) && !existsSync(promptsDir)) {\n\t\ttry {\n\t\t\trenameSync(commandsDir, promptsDir);\n\t\t\tconsole.log(chalk.green(`Migrated ${label} commands/ → prompts/`));\n\t\t\treturn true;\n\t\t} catch (err) {\n\t\t\tconsole.log(\n\t\t\t\tchalk.yellow(\n\t\t\t\t\t`Warning: Could not migrate ${label} commands/ to prompts/: ${err instanceof Error ? err.message : err}`,\n\t\t\t\t),\n\t\t\t);\n\t\t}\n\t}\n\treturn false;\n}\n\nfunction migrateKeybindingsConfigFile(): void {\n\tconst configPath = join(getAgentDir(), \"keybindings.json\");\n\tif (!existsSync(configPath)) return;\n\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(configPath, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) {\n\t\t\treturn;\n\t\t}\n\t\tconst { config, migrated } = migrateKeybindingsConfig(parsed as Record<string, unknown>);\n\t\tif (!migrated) return;\n\t\twriteFileSync(configPath, `${JSON.stringify(config, null, 2)}\\n`, \"utf-8\");\n\t} catch {\n\t\t// Ignore malformed files during migration\n\t}\n}\n\n/**\n * Move fd/rg binaries from tools/ to bin/ if they exist.\n */\nfunction migrateToolsToBin(): void {\n\tconst agentDir = getAgentDir();\n\tconst toolsDir = join(agentDir, \"tools\");\n\tconst binDir = getBinDir();\n\n\tif (!existsSync(toolsDir)) return;\n\n\tconst binaries = [\"fd\", \"rg\", \"fd.exe\", \"rg.exe\"];\n\tlet movedAny = false;\n\n\tfor (const bin of binaries) {\n\t\tconst oldPath = join(toolsDir, bin);\n\t\tconst newPath = join(binDir, bin);\n\n\t\tif (existsSync(oldPath)) {\n\t\t\tif (!existsSync(binDir)) {\n\t\t\t\tmkdirSync(binDir, { recursive: true });\n\t\t\t}\n\t\t\tif (!existsSync(newPath)) {\n\t\t\t\ttry {\n\t\t\t\t\trenameSync(oldPath, newPath);\n\t\t\t\t\tmovedAny = true;\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore errors\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// Target exists, just delete the old one\n\t\t\t\ttry {\n\t\t\t\t\trmSync?.(oldPath, { force: true });\n\t\t\t\t} catch {\n\t\t\t\t\t// Ignore\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tif (movedAny) {\n\t\tconsole.log(chalk.green(`Migrated managed binaries tools/ → bin/`));\n\t}\n}\n\n/**\n * Root-level machine-managed trust state is relocated into `state/`. If both layouts exist, valid\n * entries are merged under the canonical file's lock and canonical decisions win conflicts.\n */\nconst MAX_SESSION_NAMESPACES_TO_PRUNE = 10_000;\nconst MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE = 10_000;\nconst MAX_MIGRATION_CONFLICT_SUFFIXES = 1_000;\n\ntype MigratedTrustFile = Record<string, boolean | null>;\n\nfunction readMigratedTrustFile(path: string): MigratedTrustFile | undefined {\n\ttry {\n\t\tconst parsed = JSON.parse(readFileSync(path, \"utf-8\")) as unknown;\n\t\tif (typeof parsed !== \"object\" || parsed === null || Array.isArray(parsed)) return undefined;\n\t\tconst trust: MigratedTrustFile = {};\n\t\tfor (const [key, value] of Object.entries(parsed)) {\n\t\t\tif (value !== true && value !== false && value !== null) return undefined;\n\t\t\ttrust[key] = value;\n\t\t}\n\t\treturn trust;\n\t} catch {\n\t\treturn undefined;\n\t}\n}\n\nfunction migrateTrustState(agentDir: string): void {\n\tconst oldPath = join(agentDir, \"trust.json\");\n\tif (!existsSync(oldPath)) return;\n\tconst newPath = stateFile(agentDir, \"trust.json\");\n\tif (!existsSync(newPath)) {\n\t\tmkdirSync(dirname(newPath), { recursive: true });\n\t\trenameSync(oldPath, newPath);\n\t\treturn;\n\t}\n\n\twithFileLockSync(newPath, () => {\n\t\tconst legacy = readMigratedTrustFile(oldPath);\n\t\tconst canonical = readMigratedTrustFile(newPath);\n\t\tif (!legacy || !canonical) return;\n\t\tconst merged = { ...legacy, ...canonical };\n\t\tconst sorted = Object.fromEntries(Object.entries(merged).sort(([left], [right]) => left.localeCompare(right)));\n\t\twriteFileAtomicSync(newPath, `${JSON.stringify(sorted, null, 2)}\\n`);\n\t\tunlinkSync(oldPath);\n\t});\n}\n\nfunction migrationConflictPath(agentDir: string, legacyName: string, entryName: string): string | undefined {\n\tconst conflictDir = stateFile(agentDir, \"migration-conflicts\", legacyName);\n\tfor (let suffix = 0; suffix < MAX_MIGRATION_CONFLICT_SUFFIXES; suffix++) {\n\t\tconst name = suffix === 0 ? entryName : `${entryName}.legacy-${suffix}`;\n\t\tconst candidate = join(conflictDir, name);\n\t\tif (!existsSync(candidate)) return candidate;\n\t}\n\treturn undefined;\n}\n\n/**\n * Relocate one known legacy root without traversing its contents. A whole-root rename is O(1);\n * partial migrations scan a bounded number of top-level entries and preserve collisions under\n * state/migration-conflicts instead of overwriting either copy.\n */\nfunction migrateLegacyAgentDirectory(agentDir: string, legacyName: string, canonicalDir: string): void {\n\tconst legacyDir = join(agentDir, legacyName);\n\tif (!existsSync(legacyDir)) return;\n\tconst legacyStats = lstatSync(legacyDir);\n\tif (!legacyStats.isDirectory() || legacyStats.isSymbolicLink()) return;\n\n\tif (!existsSync(canonicalDir)) {\n\t\tmkdirSync(dirname(canonicalDir), { recursive: true });\n\t\trenameSync(legacyDir, canonicalDir);\n\t\treturn;\n\t}\n\n\tconst canonicalStats = lstatSync(canonicalDir);\n\tif (!canonicalStats.isDirectory() || canonicalStats.isSymbolicLink()) return;\n\tconst entries = readdirSync(legacyDir).slice(0, MAX_LEGACY_DIRECTORY_ENTRIES_TO_MIGRATE);\n\tfor (const entry of entries) {\n\t\tconst source = join(legacyDir, entry);\n\t\tlet target = join(canonicalDir, entry);\n\t\tif (existsSync(target)) {\n\t\t\ttarget = migrationConflictPath(agentDir, legacyName, entry) ?? \"\";\n\t\t\tif (!target) continue;\n\t\t\tmkdirSync(dirname(target), { recursive: true });\n\t\t}\n\t\ttry {\n\t\t\trenameSync(source, target);\n\t\t} catch {}\n\t}\n\n\ttry {\n\t\trmdirSync(legacyDir);\n\t} catch {}\n}\n\nfunction migrateLegacyAgentFile(agentDir: string, legacyName: string, canonicalPath: string): void {\n\tconst legacyPath = join(agentDir, legacyName);\n\tif (!existsSync(legacyPath)) return;\n\tconst legacyStats = lstatSync(legacyPath);\n\tif (!legacyStats.isFile() || legacyStats.isSymbolicLink()) return;\n\tlet target = canonicalPath;\n\tif (existsSync(target)) {\n\t\ttarget = migrationConflictPath(agentDir, \"root-files\", legacyName.replaceAll(\":\", \".\")) ?? \"\";\n\t\tif (!target) return;\n\t}\n\tmkdirSync(dirname(target), { recursive: true });\n\ttry {\n\t\trenameSync(legacyPath, target);\n\t} catch (renameError) {\n\t\t// Windows cannot rename an NTFS alternate data stream into a regular file. Preserve the\n\t\t// bytes first, then remove only the named stream; never move or rewrite the owning auth file.\n\t\twriteFileSync(target, readFileSync(legacyPath), { flag: \"wx\" });\n\t\ttry {\n\t\t\tunlinkSync(legacyPath);\n\t\t} catch {\n\t\t\ttry {\n\t\t\t\tunlinkSync(target);\n\t\t\t} catch {}\n\t\t\tthrow renameError;\n\t\t}\n\t}\n}\n\n/** Remove only empty real per-project session directories; transcript files are never retention-pruned. */\nexport function pruneEmptySessionNamespaces(agentDir: string): string[] {\n\tconst root = sessionsDir(agentDir);\n\tlet candidates: string[];\n\ttry {\n\t\tcandidates = readdirSync(root, { withFileTypes: true })\n\t\t\t.slice(0, MAX_SESSION_NAMESPACES_TO_PRUNE)\n\t\t\t.filter((entry) => entry.isDirectory() && !entry.isSymbolicLink())\n\t\t\t.map((entry) => join(root, entry.name));\n\t} catch {\n\t\treturn [];\n\t}\n\n\tconst removed: string[] = [];\n\tfor (const candidate of candidates) {\n\t\ttry {\n\t\t\tconst stats = lstatSync(candidate);\n\t\t\tif (!stats.isDirectory() || stats.isSymbolicLink() || readdirSync(candidate).length > 0) continue;\n\t\t\trmdirSync(candidate);\n\t\t\tremoved.push(candidate);\n\t\t} catch {}\n\t}\n\treturn removed;\n}\n\n/**\n * Consolidate known machine-managed layout generations. Each migration is independently guarded:\n * startup never fails because cleanup is unavailable, and unknown files/resources remain untouched.\n */\nexport function migrateAgentDirLayout(agentDir: string): void {\n\ttry {\n\t\tmigrateTrustState(agentDir);\n\t} catch {\n\t\t// Best-effort: startup must not fail because one straggler could not be relocated.\n\t}\n\ttry {\n\t\tmigrateLegacyContextStores(agentDir);\n\t\tpruneContextStores(agentDir);\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"backups\", configBackupsDir(agentDir));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"resource-profiles\", directoryProfilesDir(agentDir));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"auto-learn\", stateFile(agentDir, \"legacy-layout\", \"auto-learn\"));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentDirectory(agentDir, \"tmp\", stateFile(agentDir, \"legacy-layout\", \"tmp\"));\n\t} catch {}\n\ttry {\n\t\tmigrateLegacyAgentFile(\n\t\t\tagentDir,\n\t\t\t\"auth.json:Zone.Identifier\",\n\t\t\tstateFile(agentDir, \"legacy-layout\", \"sidecars\", \"auth.json.Zone.Identifier\"),\n\t\t);\n\t} catch {}\n\tpruneEmptySessionNamespaces(agentDir);\n}\n\n/**\n * Check for deprecated hooks/ and tools/ directories.\n * Note: tools/ may contain fd/rg binaries extracted by pi, so only warn if it has other files.\n */\nfunction checkDeprecatedExtensionDirs(baseDir: string, label: string): string[] {\n\tconst hooksDir = join(baseDir, \"hooks\");\n\tconst toolsDir = join(baseDir, \"tools\");\n\tconst warnings: string[] = [];\n\n\tif (existsSync(hooksDir)) {\n\t\twarnings.push(`${label} hooks/ directory found. Hooks have been renamed to extensions.`);\n\t}\n\n\tif (existsSync(toolsDir)) {\n\t\t// Check if tools/ contains anything other than fd/rg (which are auto-extracted binaries)\n\t\ttry {\n\t\t\tconst entries = readdirSync(toolsDir);\n\t\t\tconst customTools = entries.filter((e) => {\n\t\t\t\tconst lower = e.toLowerCase();\n\t\t\t\treturn (\n\t\t\t\t\tlower !== \"fd\" && lower !== \"rg\" && lower !== \"fd.exe\" && lower !== \"rg.exe\" && !e.startsWith(\".\") // Ignore .DS_Store and other hidden files\n\t\t\t\t);\n\t\t\t});\n\t\t\tif (customTools.length > 0) {\n\t\t\t\twarnings.push(\n\t\t\t\t\t`${label} tools/ directory contains custom tools. Custom tools have been merged into extensions.`,\n\t\t\t\t);\n\t\t\t}\n\t\t} catch {\n\t\t\t// Ignore read errors\n\t\t}\n\t}\n\n\treturn warnings;\n}\n\n/**\n * Run extension system migrations (commands→prompts) and collect warnings about deprecated directories.\n */\nfunction migrateExtensionSystem(cwd: string): string[] {\n\tconst agentDir = getAgentDir();\n\tconst projectDir = join(cwd, CONFIG_DIR_NAME);\n\n\t// Migrate commands/ to prompts/\n\tmigrateCommandsToPrompts(agentDir, \"Global\");\n\tmigrateCommandsToPrompts(projectDir, \"Project\");\n\n\t// Check for deprecated directories\n\tconst warnings = [\n\t\t...checkDeprecatedExtensionDirs(agentDir, \"Global\"),\n\t\t...checkDeprecatedExtensionDirs(projectDir, \"Project\"),\n\t];\n\n\treturn warnings;\n}\n\n/**\n * Print deprecation warnings and wait for keypress.\n */\nexport async function showDeprecationWarnings(warnings: string[]): Promise<void> {\n\tif (warnings.length === 0) return;\n\n\tfor (const warning of warnings) {\n\t\tconsole.log(chalk.yellow(`Warning: ${warning}`));\n\t}\n\tconsole.log(chalk.yellow(`\\nMove your extensions to the extensions/ directory.`));\n\tconsole.log(chalk.yellow(`Migration guide: ${MIGRATION_GUIDE_URL}`));\n\tconsole.log(chalk.yellow(`Documentation: ${EXTENSIONS_DOC_URL}`));\n\tif (!process.stdin.isTTY || !process.stdout.isTTY) {\n\t\tconsole.log();\n\t\treturn;\n\t}\n\tconsole.log(chalk.dim(`\\nPress any key to continue...`));\n\n\tawait new Promise<void>((resolve) => {\n\t\tlet settled = false;\n\t\tconst finish = () => {\n\t\t\tif (settled) return;\n\t\t\tsettled = true;\n\t\t\tprocess.stdin.removeListener(\"data\", finish);\n\t\t\tprocess.stdin.removeListener(\"end\", finish);\n\t\t\tprocess.stdin.removeListener(\"error\", finish);\n\t\t\tprocess.stdin.setRawMode?.(false);\n\t\t\tprocess.stdin.pause();\n\t\t\tresolve();\n\t\t};\n\t\tprocess.stdin.setRawMode?.(true);\n\t\tprocess.stdin.resume();\n\t\tprocess.stdin.once(\"data\", finish);\n\t\tprocess.stdin.once(\"end\", finish);\n\t\tprocess.stdin.once(\"error\", finish);\n\t});\n\tconsole.log();\n}\n\n/**\n * Run all migrations. Called once on startup.\n *\n * @returns Object with migration results and deprecation warnings\n */\nexport function runMigrations(cwd: string): {\n\tmigratedAuthProviders: string[];\n\tdeprecationWarnings: string[];\n} {\n\tmigrateAgentDirLayout(getAgentDir());\n\tconst migratedAuthProviders = migrateAuthToAuthJson();\n\tmigrateExplicitEnvVarConfigValues();\n\tmigrateSessionsFromAgentRoot();\n\tmigrateToolsToBin();\n\tmigrateKeybindingsConfigFile();\n\tconst deprecationWarnings = migrateExtensionSystem(cwd);\n\treturn { migratedAuthProviders, deprecationWarnings };\n}\n"]}

package/dist/modes/interactive/auto-learn-controller.d.ts

@@ -85,6 +85,7 @@ export declare class AutoLearnController {
     private _pendingReflectionText;
     private static readonly NATIVE_REFLECTION_MIN_INTERVAL_MS;
     private static readonly PENDING_REFLECTION_MAX_CHARS;
+    private _taskContractStreak;
     private readonly deps;
     constructor(deps: AutoLearnControllerDeps);
     private get session();
@@ -138,7 +139,7 @@ export declare class AutoLearnController {
     private buildAutonomyReviewDigest;
     private evaluateAutonomyReview;
     /**
-     * Native reflection (R2) is the in-process replacement for the buggy `continuous-learning`
+     * Native reflection is the in-process replacement for the buggy `continuous-learning`
      * subprocess. It runs when auto-learn is enabled and is not killed via `PI_NATIVE_REFLECTION=0`.
      */
     isNativeReflectionEnabled(): boolean;
@@ -159,6 +160,20 @@ export declare class AutoLearnController {
     /** Buffer a debounce-skipped turn's text so its learning is folded into the next pass (bug #29). */
     private _bufferPendingReflection;
     private _drainPendingReflection;
+    /**
+     * Cheap turn-boundary task_steps contract check. Reads the current task_steps snapshot,
+     * advances the pure `checkTaskStepsContract` streak, and — on the exact turn a sustained
+     * violation first reaches the threshold — delivers a ONE-LINE advisory harness note through the
+     * session's existing next-turn message surface (`sendCustomMessage(..., {deliverAs:"nextTurn"})`,
+     * the same mechanism `_pendingNextTurnMessages` already injects `memory_context`/
+     * `task_steps_context` pages through). Zero model calls; a delivery failure is swallowed so this
+     * best-effort nudge can never disrupt the turn.
+     *
+     * Called from both `maybeRunNativeReflection` and `maybeStartAutoLearn` — the mutually exclusive
+     * `agent_end` branches in interactive-mode.ts — so it runs on every turn regardless of whether
+     * native reflection or legacy auto-learn is enabled, without adding a new turn-boundary hook.
+     */
+    private checkTaskStepsContractNudge;
     maybeRunNativeReflection(messages: AgentMessage[]): void;
     maybeStartAutoLearn(): boolean;
     maybeStartAutonomyReview(messages: AgentMessage[]): boolean;