iosm-cli 0.3.0 → 0.3.2

package/CHANGELOG.md

@@ -7,6 +7,49 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.2] - 2026-04-05
+
+### Fixed
+
+- **Playbook filename canonicalization** — `/init` and `iosm init` now normalize lowercase variants (`agents.md`, `iosm.md`) to canonical `AGENTS.md` and `IOSM.md`
+- **Cross-platform case handling** — implemented robust case-only rename flow (with temporary hop) to reliably normalize filenames on case-insensitive filesystems
+- **Profile context continuity** — `IOSM.md` context is now kept loaded in the resource layer to avoid context loss after runtime profile switching
+
+### Changed
+
+- **Standard init path resolution** — standard `/init` now resolves and writes through canonical playbook path before reading/updating repository guidance
+- **IOSM guide writers** — IOSM/AGENTS guide writers now enforce canonical path selection prior to write operations
+
+### Tests
+
+- Added regression tests for lowercase-to-canonical playbook rename behavior in:
+  - iosm guide writer flow
+  - iosm init flow
+  - interactive standard `/init` flow
+- Updated resource-loader profile test expectations for runtime profile switching behavior
+
+## [0.3.1] - 2026-04-05
+
+### Added
+
+- **Profile-aware `/init` flow** — `/init` now follows active profile semantics: `full/plan/meta` updates `AGENTS.md`; `iosm` initializes and synchronizes both `AGENTS.md` and `IOSM.md`
+- **AGENTS managed sync block for IOSM** — introduced deterministic managed section in `AGENTS.md` during IOSM init, preserving user-authored content outside the managed block
+
+### Changed
+
+- **IOSM init file sync contract** — `iosm init` now performs guaranteed create/update for both `AGENTS.md` and `IOSM.md` to avoid missing physical playbook files
+- **Interactive init control flow** — added dedicated standard-init session tracking with explicit “already running” guard and interrupt-safe cancellation path
+- **CLI init status output** — `iosm init` now reports per-file state for `AGENTS.md` and `IOSM.md` (`created/updated/skipped/unchanged`)
+
+### Documentation
+
+- Updated README release marker and highlights to `0.3.1`
+- Updated `docs/getting-started.md` and `docs/interactive-mode.md` to document profile-scoped `/init` behavior
+
+### Tests
+
+- Expanded coverage for IOSM/AGENTS guide writers and profile-aware `/init` behavior in interactive and init test suites
+
 ## [0.3.0] - 2026-04-05
 
 ### Added

package/README.md

@@ -1,6 +1,6 @@
 <div align="center">
 
-<h1>IOSM CLI 0.3.0</h1>
+<h1>IOSM CLI 0.3.2</h1>
 
 <p><strong>Terminal-native AI runtime for controlled, measurable engineering work on real codebases.</strong></p>
 
@@ -32,13 +32,13 @@ It is not a chat interface. It is a runtime.
 
 ---
 
-## ✦ What's New in 0.3.0
+## ✦ What's New in 0.3.2
 
-- Interactive UI refresh with unified framed windows for user, assistant, tool, and orchestration output
-- Redesigned input area with mode-aware header (`input >`, `command /`, `bash !`) and consistent spacing
-- Improved reasoning UX: collapsed reasoning preview with live spinner while assistant is streaming
-- Added color-coded execution surfaces: green-framed tool output and orange-framed orchestration panel
-- Added compact footer mode toggle in interactive settings
+- Canonical playbook filenames are now enforced during init flows: lowercase variants (`agents.md`, `iosm.md`) are automatically renamed to `AGENTS.md` and `IOSM.md`
+- Standard `/init` now always reads/writes through canonical `AGENTS.md` path, including existing repositories with mixed filename casing
+- IOSM guide writers now canonicalize `AGENTS.md` and `IOSM.md` before updates for consistent context loading across sessions
+- Improved runtime profile switching continuity by keeping `IOSM.md` context loaded in resource layer while preserving profile-aware prompt/UI filtering
+- Added regression tests covering filename normalization and profile-switch context behavior
 
 ## ✦ Major Additions in 0.2.16
 

package/dist/core/resource-loader.d.ts.map

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+{"version":3,"file":"resource-loader.d.ts","sourceRoot":"","sources":["../../src/core/resource-loader.ts"],"names":[],"mappings":"AAMA,OAAO,EAAqB,KAAK,KAAK,EAAE,MAAM,qCAAqC,CAAC;AACpF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAE3D,YAAY,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAE9E,OAAO,EAAkB,KAAK,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAE/D,OAAO,KAAK,EAAa,gBAAgB,EAAoB,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AACjH,OAAO,EAAyB,KAAK,YAAY,EAAE,MAAM,sBAAsB,CAAC;AAChF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAE5D,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAEzC,OAAO,EAAqC,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAEvF,MAAM,WAAW,sBAAsB;IACtC,UAAU,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;IAC7D,WAAW,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;IAC9D,UAAU,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;CAC7D;AAED,MAAM,MAAM,cAAc,GAAG,UAAU,GAAG,MAAM,CAAC;AAEjD,MAAM,WAAW,cAAc;IAC9B,aAAa,IAAI,oBAAoB,CAAC;IACtC,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IACpE,UAAU,IAAI;QAAE,OAAO,EAAE,cAAc,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IAC/E,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IACpE,cAAc,IAAI;QAAE,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE,CAAC;IAC5E,eAAe,IAAI,MAAM,GAAG,SAAS,CAAC;IACtC,qBAAqB,IAAI,MAAM,EAAE,CAAC;IAClC,QAAQ,CAAC,IAAI,iBAAiB,CAAC;IAC/B,eAAe,IAAI,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC;IAC7C,eAAe,CAAC,KAAK,EAAE,sBAAsB,GAAG,IAAI,CAAC;IACrD,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;CACxB;AAgQD,MAAM,WAAW,4BAA4B;IAC5C,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,cAAc,CAAC,EAAE,cAAc,GAAG,MAAM,CAAC;IACzC,eAAe,CAAC,EAAE,eAAe,CAAC;IAClC,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,wBAAwB,CAAC,EAAE,MAAM,EAAE,CAAC;IACpC,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,6BAA6B,CAAC,EAAE,MAAM,EAAE,CAAC;IACzC,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,kBAAkB,CAAC,EAAE,gBAAgB,EAAE,CAAC;IACxC,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,kBAAkB,CAAC,EAAE,CAAC,IAAI,EAAE,oBAAoB,KAAK,oBAAoB,CAAC;IAC1E,cAAc,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAClF,MAAM,EAAE,KAAK,EAAE,CAAC;QAChB,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,eAAe,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,OAAO,EAAE,cAAc,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAC7F,OAAO,EAAE,cAAc,EAAE,CAAC;QAC1B,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,cAAc,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAClF,MAAM,EAAE,KAAK,EAAE,CAAC;QAChB,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,mBAAmB,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE,KAAK;QAC1F,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KACtD,CAAC;IACF,oBAAoB,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,KAAK,MAAM,GAAG,SAAS,CAAC;IACxE,0BAA0B,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,MAAM,EAAE,CAAC;CAC1D;AAED,qBAAa,qBAAsB,YAAW,cAAc;IAC3D,OAAO,CAAC,GAAG,CAAS;IACpB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,eAAe,CAAC,CAAS;IACjC,OAAO,CAAC,cAAc,CAAiB;IACvC,OAAO,CAAC,eAAe,CAAkB;IACzC,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,cAAc,CAAwB;IAC9C,OAAO,CAAC,wBAAwB,CAAW;IAC3C,OAAO,CAAC,oBAAoB,CAAW;IACvC,OAAO,CAAC,6BAA6B,CAAW;IAChD,OAAO,CAAC,oBAAoB,CAAW;IACvC,OAAO,CAAC,kBAAkB,CAAqB;IAC/C,OAAO,CAAC,YAAY,CAAU;IAC9B,OAAO,CAAC,QAAQ,CAAU;IAC1B,OAAO,CAAC,iBAAiB,CAAU;IACnC,OAAO,CAAC,QAAQ,CAAU;IAC1B,OAAO,CAAC,kBAAkB,CAAC,CAAS;IACpC,OAAO,CAAC,wBAAwB,CAAC,CAAS;IAC1C,OAAO,CAAC,kBAAkB,CAAC,CAAuD;IAClF,OAAO,CAAC,cAAc,CAAC,CAGrB;IACF,OAAO,CAAC,eAAe,CAAC,CAGtB;IACF,OAAO,CAAC,cAAc,CAAC,CAGrB;IACF,OAAO,CAAC,mBAAmB,CAAC,CAE1B;IACF,OAAO,CAAC,oBAAoB,CAAC,CAAmD;IAChF,OAAO,CAAC,0BAA0B,CAAC,CAA+B;IAElE,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,MAAM,CAAU;IACxB,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,OAAO,CAAmB;IAClC,OAAO,CAAC,iBAAiB,CAAuB;IAChD,OAAO,CAAC,MAAM,CAAU;IACxB,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,WAAW,CAA2C;IAC9D,OAAO,CAAC,YAAY,CAAC,CAAS;IAC9B,OAAO,CAAC,kBAAkB,CAAW;IACrC,OAAO,CAAC,KAAK,CAAoB;IACjC,OAAO,CAAC,YAAY,CAA4B;IAChD,OAAO,CAAC,cAAc,CAAW;IACjC,OAAO,CAAC,eAAe,CAAW;IAClC,OAAO,CAAC,cAAc,CAAW;gBAErB,OAAO,EAAE,4BAA4B;IAgDjD,aAAa,IAAI,oBAAoB;IAIrC,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE;IAInE,UAAU,IAAI;QAAE,OAAO,EAAE,cAAc,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE;IAI9E,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE;IAInE,cAAc,IAAI;QAAE,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE;IAI3E,eAAe,IAAI,MAAM,GAAG,SAAS;IAIrC,qBAAqB,IAAI,MAAM,EAAE;IAIjC,QAAQ,IAAI,iBAAiB;IAI7B,eAAe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package/dist/core/resource-loader.js

@@ -172,8 +172,10 @@ function loadProjectContextFiles(options = {}) {
     const resolvedCwd = options.cwd ?? process.cwd();
     const resolvedAgentDir = options.agentDir ?? getAgentDir();
     const resolvedHomeDir = options.homeDir ?? homedir();
-    const contextProfile = normalizeContextProfile(options.contextProfile);
-    const includeIosm = contextProfile === "iosm";
+    // Keep IOSM context files loaded regardless of startup profile.
+    // The active profile still controls what is injected into prompts and shown in UI.
+    // This prevents context loss when operators switch profile at runtime.
+    const includeIosm = true;
     const organizationDirEnv = options.organizationDir ?? process.env.IOSM_ORG_DIR ?? process.env.PI_ORG_DIR;
     const resolvedOrganizationDir = organizationDirEnv
         ? resolve(expandHomePath(organizationDirEnv, resolvedHomeDir))

package/dist/core/resource-loader.js.map

@@ -1 +1 @@
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{ existsSync, lstatSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { join, resolve, sep } from \"node:path\";\nimport chalk from \"chalk\";\nimport { CONFIG_DIR_NAME, getAgentDir } from \"../config.js\";\nimport { buildIosmContextBlock } from \"../iosm/context-loader.js\";\nimport { loadThemeFromPath, type Theme } from \"../modes/interactive/theme/theme.js\";\nimport type { ResourceDiagnostic } from \"./diagnostics.js\";\n\nexport type { ResourceCollision, ResourceDiagnostic } from \"./diagnostics.js\";\n\nimport { createEventBus, type EventBus } from \"./event-bus.js\";\nimport { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from \"./extensions/loader.js\";\nimport type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from \"./extensions/types.js\";\nimport { DefaultPackageManager, type PathMetadata } from \"./package-manager.js\";\nimport type { PromptTemplate } from \"./prompt-templates.js\";\nimport { loadPromptTemplates } from \"./prompt-templates.js\";\nimport { SettingsManager } from \"./settings-manager.js\";\nimport type { Skill } from \"./skills.js\";\nimport { loadSkills } from \"./skills.js\";\nimport { emptyHooksConfig, loadHooksConfig, type LoadedHooksConfig } from \"./hooks.js\";\n\nexport interface ResourceExtensionPaths {\n\tskillPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tpromptPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tthemePaths?: Array<{ path: string; metadata: PathMetadata }>;\n}\n\nexport type ContextProfile = \"standard\" | \"iosm\";\n\nexport interface ResourceLoader {\n\tgetExtensions(): LoadExtensionsResult;\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> };\n\tgetSystemPrompt(): string | undefined;\n\tgetAppendSystemPrompt(): string[];\n\tgetHooks?(): LoadedHooksConfig;\n\tgetPathMetadata(): Map<string, PathMetadata>;\n\textendResources(paths: ResourceExtensionPaths): void;\n\treload(): Promise<void>;\n}\n\nfunction resolvePromptInput(input: string | undefined, description: string): string | undefined {\n\tif (!input) {\n\t\treturn undefined;\n\t}\n\n\tif (existsSync(input)) {\n\t\ttry {\n\t\t\treturn readFileSync(input, \"utf-8\");\n\t\t} catch (error) {\n\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${description} file ${input}: ${error}`));\n\t\t\treturn input;\n\t\t}\n\t}\n\n\treturn input;\n}\n\nfunction normalizeContextProfile(profile: string | undefined): ContextProfile {\n\treturn profile?.toLowerCase() === \"iosm\" ? \"iosm\" : \"standard\";\n}\n\nfunction expandHomePath(pathValue: string, homeDir: string): string {\n\tif (pathValue === \"~\") return homeDir;\n\tif (pathValue.startsWith(\"~/\")) return join(homeDir, pathValue.slice(2));\n\treturn pathValue;\n}\n\nfunction loadContextFilesFromDir(\n\tdir: string,\n\toptions: { includeAgents?: boolean; includeIosm?: boolean } = {},\n): Array<{ path: string; content: string }> {\n\tconst includeAgents = options.includeAgents !== false;\n\tconst includeIosm = options.includeIosm === true;\n\tconst candidates = [\n\t\t...(includeAgents ? [\"AGENTS.md\"] : []),\n\t\t...(includeIosm ? [\"IOSM.md\"] : []),\n\t];\n\tconst files: Array<{ path: string; content: string }> = [];\n\tfor (const filename of candidates) {\n\t\tconst filePath = join(dir, filename);\n\t\tif (existsSync(filePath)) {\n\t\t\ttry {\n\t\t\t\tconst content = readFileSync(filePath, \"utf-8\");\n\t\t\t\tfiles.push({\n\t\t\t\t\tpath: filePath,\n\t\t\t\t\tcontent: filename === \"IOSM.md\" ? buildIosmContextBlock(content) : content,\n\t\t\t\t});\n\t\t\t} catch (error) {\n\t\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${filePath}: ${error}`));\n\t\t\t}\n\t\t}\n\t}\n\treturn files;\n}\n\nfunction listMarkdownFilesRecursive(dir: string): string[] {\n\tlet entries: string[] = [];\n\ttry {\n\t\tentries = readdirSync(dir).sort((a, b) => a.localeCompare(b));\n\t} catch {\n\t\treturn [];\n\t}\n\n\tconst files: string[] = [];\n\tfor (const entry of entries) {\n\t\tconst filePath = join(dir, entry);\n\t\tlet stat;\n\t\ttry {\n\t\t\tconst lstat = lstatSync(filePath);\n\t\t\tif (lstat.isSymbolicLink()) continue;\n\t\t\tstat = statSync(filePath);\n\t\t} catch {\n\t\t\tcontinue;\n\t\t}\n\t\tif (stat.isDirectory()) {\n\t\t\tfiles.push(...listMarkdownFilesRecursive(filePath));\n\t\t\tcontinue;\n\t\t}\n\t\tif (stat.isFile() && entry.toLowerCase().endsWith(\".md\")) {\n\t\t\tfiles.push(filePath);\n\t\t}\n\t}\n\treturn files;\n}\n\nfunction loadExpandedMemoryFile(\n\tfilePath: string,\n\tmaxDepth: number = 5,\n\tvisited: Set<string> = new Set(),\n): string | undefined {\n\tconst resolvedPath = resolve(filePath);\n\tif (visited.has(resolvedPath)) return undefined;\n\tif (!existsSync(resolvedPath)) return undefined;\n\tif (maxDepth < 0) return undefined;\n\n\tvisited.add(resolvedPath);\n\tlet raw: string;\n\ttry {\n\t\traw = readFileSync(resolvedPath, \"utf-8\");\n\t} catch {\n\t\treturn undefined;\n\t}\n\n\tconst baseDir = resolve(resolvedPath, \"..\");\n\tconst lines = raw.split(/\\r?\\n/);\n\tconst expanded: string[] = [];\n\n\tfor (const line of lines) {\n\t\tconst trimmed = line.trim();\n\t\tconst importMatch = trimmed.match(/^@(?:import\\s+)?(.+)$/i);\n\t\tif (!importMatch) {\n\t\t\texpanded.push(line);\n\t\t\tcontinue;\n\t\t}\n\n\t\tconst importTargetRaw = importMatch[1]?.trim();\n\t\tif (!importTargetRaw) continue;\n\t\tconst importTarget = importTargetRaw.replace(/^[\"']|[\"']$/g, \"\");\n\t\tconst importPath = resolve(baseDir, importTarget);\n\t\tconst imported = loadExpandedMemoryFile(importPath, maxDepth - 1, visited);\n\t\tif (imported && imported.trim().length > 0) {\n\t\t\texpanded.push(imported.trimEnd());\n\t\t}\n\t}\n\n\treturn expanded.join(\"\\n\");\n}\n\nfunction loadMemoryContextFilesFromConfigDir(configDir: string): Array<{ path: string; content: string }> {\n\tconst result: Array<{ path: string; content: string }> = [];\n\tconst memoryRootFile = join(configDir, \"memory.md\");\n\tconst expandedRoot = loadExpandedMemoryFile(memoryRootFile);\n\tif (expandedRoot && expandedRoot.trim().length > 0) {\n\t\tresult.push({ path: memoryRootFile, content: expandedRoot });\n\t}\n\n\tconst memoryDir = join(configDir, \"memory\");\n\tif (!existsSync(memoryDir)) return result;\n\tfor (const filePath of listMarkdownFilesRecursive(memoryDir)) {\n\t\tconst expanded = loadExpandedMemoryFile(filePath);\n\t\tif (!expanded || expanded.trim().length === 0) continue;\n\t\tresult.push({ path: filePath, content: expanded });\n\t}\n\n\treturn result;\n}\n\nfunction loadMemoryContextFilesFromRoot(rootDir: string): Array<{ path: string; content: string }> {\n\treturn loadMemoryContextFilesFromConfigDir(join(rootDir, \".iosm\"));\n}\n\nfunction loadMemoryContextFilesFromAgentDir(agentDir: string): Array<{ path: string; content: string }> {\n\tconst files: Array<{ path: string; content: string }> = [];\n\tconst seen = new Set<string>();\n\tconst addUnique = (entry: { path: string; content: string }) => {\n\t\tconst resolvedPath = resolve(entry.path);\n\t\tif (seen.has(resolvedPath)) return;\n\t\tseen.add(resolvedPath);\n\t\tfiles.push(entry);\n\t};\n\n\tfor (const entry of loadMemoryContextFilesFromConfigDir(agentDir)) addUnique(entry);\n\tfor (const entry of loadMemoryContextFilesFromRoot(agentDir)) addUnique(entry);\n\treturn files;\n}\n\nfunction loadProjectContextFiles(\n\toptions: {\n\t\tcwd?: string;\n\t\tagentDir?: string;\n\t\thomeDir?: string;\n\t\torganizationDir?: string;\n\t\tcontextProfile?: ContextProfile | string;\n\t} = {},\n): Array<{ path: string; content: string }> {\n\tconst resolvedCwd = options.cwd ?? process.cwd();\n\tconst resolvedAgentDir = options.agentDir ?? getAgentDir();\n\tconst resolvedHomeDir = options.homeDir ?? homedir();\n\tconst contextProfile = normalizeContextProfile(options.contextProfile);\n\tconst includeIosm = contextProfile === \"iosm\";\n\tconst organizationDirEnv = options.organizationDir ?? process.env.IOSM_ORG_DIR ?? process.env.PI_ORG_DIR;\n\tconst resolvedOrganizationDir = organizationDirEnv\n\t\t? resolve(expandHomePath(organizationDirEnv, resolvedHomeDir))\n\t\t: undefined;\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst seenPaths = new Set<string>();\n\tconst appendUnique = (entry: { path: string; content: string }) => {\n\t\tif (seenPaths.has(entry.path)) return;\n\t\tcontextFiles.push(entry);\n\t\tseenPaths.add(entry.path);\n\t};\n\n\tif (resolvedOrganizationDir) {\n\t\tfor (const organizationContext of loadContextFilesFromDir(resolvedOrganizationDir, { includeIosm })) {\n\t\t\tappendUnique(organizationContext);\n\t\t}\n\t\tfor (const organizationMemory of loadMemoryContextFilesFromRoot(resolvedOrganizationDir)) {\n\t\t\tappendUnique(organizationMemory);\n\t\t}\n\t}\n\n\tconst userConfigDir = join(resolvedHomeDir, \".iosm\");\n\tfor (const userContext of loadContextFilesFromDir(userConfigDir, { includeIosm })) {\n\t\tappendUnique(userContext);\n\t}\n\tfor (const userMemory of loadMemoryContextFilesFromRoot(resolvedHomeDir)) {\n\t\tappendUnique(userMemory);\n\t}\n\n\tfor (const globalContext of loadContextFilesFromDir(resolvedAgentDir, { includeIosm })) {\n\t\tappendUnique(globalContext);\n\t}\n\tfor (const globalMemory of loadMemoryContextFilesFromAgentDir(resolvedAgentDir)) {\n\t\tappendUnique(globalMemory);\n\t}\n\n\tconst ancestorContextFiles: Array<{ path: string; content: string }> = [];\n\n\tlet currentDir = resolvedCwd;\n\tconst root = resolve(\"/\");\n\n\twhile (true) {\n\t\tconst contextFilesInDir = loadContextFilesFromDir(currentDir, { includeIosm });\n\t\tfor (let index = contextFilesInDir.length - 1; index >= 0; index--) {\n\t\t\tconst contextFile = contextFilesInDir[index];\n\t\t\tif (seenPaths.has(contextFile.path)) {\n\t\t\t\tcontinue;\n\t\t\t}\n\t\t\tancestorContextFiles.unshift(contextFile);\n\t\t\tseenPaths.add(contextFile.path);\n\t\t}\n\t\tconst memoryFilesInDir = loadMemoryContextFilesFromRoot(currentDir);\n\t\tfor (let index = memoryFilesInDir.length - 1; index >= 0; index--) {\n\t\t\tconst memoryFile = memoryFilesInDir[index];\n\t\t\tif (seenPaths.has(memoryFile.path)) continue;\n\t\t\tancestorContextFiles.unshift(memoryFile);\n\t\t\tseenPaths.add(memoryFile.path);\n\t\t}\n\n\t\tif (currentDir === root) break;\n\n\t\tconst parentDir = resolve(currentDir, \"..\");\n\t\tif (parentDir === currentDir) break;\n\t\tcurrentDir = parentDir;\n\t}\n\n\tcontextFiles.push(...ancestorContextFiles);\n\n\treturn contextFiles;\n}\n\nexport interface DefaultResourceLoaderOptions {\n\tcwd?: string;\n\tagentDir?: string;\n\thomeDir?: string;\n\torganizationDir?: string;\n\tcontextProfile?: ContextProfile | string;\n\tsettingsManager?: SettingsManager;\n\teventBus?: EventBus;\n\tadditionalExtensionPaths?: string[];\n\tadditionalSkillPaths?: string[];\n\tadditionalPromptTemplatePaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoThemes?: boolean;\n\tsystemPrompt?: string;\n\tappendSystemPrompt?: string;\n\textensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tskillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tpromptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tthemesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tagentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tsystemPromptOverride?: (base: string | undefined) => string | undefined;\n\tappendSystemPromptOverride?: (base: string[]) => string[];\n}\n\nexport class DefaultResourceLoader implements ResourceLoader {\n\tprivate cwd: string;\n\tprivate agentDir: string;\n\tprivate homeDir: string;\n\tprivate organizationDir?: string;\n\tprivate contextProfile: ContextProfile;\n\tprivate settingsManager: SettingsManager;\n\tprivate eventBus: EventBus;\n\tprivate packageManager: DefaultPackageManager;\n\tprivate additionalExtensionPaths: string[];\n\tprivate additionalSkillPaths: string[];\n\tprivate additionalPromptTemplatePaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noThemes: boolean;\n\tprivate systemPromptSource?: string;\n\tprivate appendSystemPromptSource?: string;\n\tprivate extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tprivate skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tprivate systemPromptOverride?: (base: string | undefined) => string | undefined;\n\tprivate appendSystemPromptOverride?: (base: string[]) => string[];\n\n\tprivate extensionsResult: LoadExtensionsResult;\n\tprivate skills: Skill[];\n\tprivate skillDiagnostics: ResourceDiagnostic[];\n\tprivate prompts: PromptTemplate[];\n\tprivate promptDiagnostics: ResourceDiagnostic[];\n\tprivate themes: Theme[];\n\tprivate themeDiagnostics: ResourceDiagnostic[];\n\tprivate agentsFiles: Array<{ path: string; content: string }>;\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate hooks: LoadedHooksConfig;\n\tprivate pathMetadata: Map<string, PathMetadata>;\n\tprivate lastSkillPaths: string[];\n\tprivate lastPromptPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = options.cwd ?? process.cwd();\n\t\tthis.agentDir = options.agentDir ?? getAgentDir();\n\t\tthis.homeDir = options.homeDir ?? homedir();\n\t\tthis.organizationDir = options.organizationDir;\n\t\tthis.contextProfile = normalizeContextProfile(options.contextProfile);\n\t\tthis.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);\n\t\tthis.eventBus = options.eventBus ?? createEventBus();\n\t\tthis.packageManager = new DefaultPackageManager({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\tsettingsManager: this.settingsManager,\n\t\t});\n\t\tthis.additionalExtensionPaths = options.additionalExtensionPaths ?? [];\n\t\tthis.additionalSkillPaths = options.additionalSkillPaths ?? [];\n\t\tthis.additionalPromptTemplatePaths = options.additionalPromptTemplatePaths ?? [];\n\t\tthis.additionalThemePaths = options.additionalThemePaths ?? [];\n\t\tthis.extensionFactories = options.extensionFactories ?? [];\n\t\tthis.noExtensions = options.noExtensions ?? false;\n\t\tthis.noSkills = options.noSkills ?? false;\n\t\tthis.noPromptTemplates = options.noPromptTemplates ?? false;\n\t\tthis.noThemes = options.noThemes ?? false;\n\t\tthis.systemPromptSource = options.systemPrompt;\n\t\tthis.appendSystemPromptSource = options.appendSystemPrompt;\n\t\tthis.extensionsOverride = options.extensionsOverride;\n\t\tthis.skillsOverride = options.skillsOverride;\n\t\tthis.promptsOverride = options.promptsOverride;\n\t\tthis.themesOverride = options.themesOverride;\n\t\tthis.agentsFilesOverride = options.agentsFilesOverride;\n\t\tthis.systemPromptOverride = options.systemPromptOverride;\n\t\tthis.appendSystemPromptOverride = options.appendSystemPromptOverride;\n\n\t\tthis.extensionsResult = { extensions: [], errors: [], runtime: createExtensionRuntime() };\n\t\tthis.skills = [];\n\t\tthis.skillDiagnostics = [];\n\t\tthis.prompts = [];\n\t\tthis.promptDiagnostics = [];\n\t\tthis.themes = [];\n\t\tthis.themeDiagnostics = [];\n\t\tthis.agentsFiles = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.hooks = emptyHooksConfig();\n\t\tthis.pathMetadata = new Map();\n\t\tthis.lastSkillPaths = [];\n\t\tthis.lastPromptPaths = [];\n\t\tthis.lastThemePaths = [];\n\t}\n\n\tgetExtensions(): LoadExtensionsResult {\n\t\treturn this.extensionsResult;\n\t}\n\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { skills: this.skills, diagnostics: this.skillDiagnostics };\n\t}\n\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { prompts: this.prompts, diagnostics: this.promptDiagnostics };\n\t}\n\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { themes: this.themes, diagnostics: this.themeDiagnostics };\n\t}\n\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> } {\n\t\treturn { agentsFiles: this.agentsFiles };\n\t}\n\n\tgetSystemPrompt(): string | undefined {\n\t\treturn this.systemPrompt;\n\t}\n\n\tgetAppendSystemPrompt(): string[] {\n\t\treturn this.appendSystemPrompt;\n\t}\n\n\tgetHooks(): LoadedHooksConfig {\n\t\treturn this.hooks;\n\t}\n\n\tgetPathMetadata(): Map<string, PathMetadata> {\n\t\treturn this.pathMetadata;\n\t}\n\n\textendResources(paths: ResourceExtensionPaths): void {\n\t\tconst skillPaths = this.normalizeExtensionPaths(paths.skillPaths ?? []);\n\t\tconst promptPaths = this.normalizeExtensionPaths(paths.promptPaths ?? []);\n\t\tconst themePaths = this.normalizeExtensionPaths(paths.themePaths ?? []);\n\n\t\tif (skillPaths.length > 0) {\n\t\t\tthis.lastSkillPaths = this.mergePaths(\n\t\t\t\tthis.lastSkillPaths,\n\t\t\t\tskillPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateSkillsFromPaths(this.lastSkillPaths, skillPaths);\n\t\t}\n\n\t\tif (promptPaths.length > 0) {\n\t\t\tthis.lastPromptPaths = this.mergePaths(\n\t\t\t\tthis.lastPromptPaths,\n\t\t\t\tpromptPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updatePromptsFromPaths(this.lastPromptPaths, promptPaths);\n\t\t}\n\n\t\tif (themePaths.length > 0) {\n\t\t\tthis.lastThemePaths = this.mergePaths(\n\t\t\t\tthis.lastThemePaths,\n\t\t\t\tthemePaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateThemesFromPaths(this.lastThemePaths, themePaths);\n\t\t}\n\t}\n\n\tasync reload(): Promise<void> {\n\t\tconst resolvedPaths = await this.packageManager.resolve();\n\t\tconst cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {\n\t\t\ttemporary: true,\n\t\t});\n\n\t\t// Helper to extract enabled paths and store metadata\n\t\tconst getEnabledResources = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): Array<{ path: string; enabled: boolean; metadata: PathMetadata }> => {\n\t\t\tfor (const r of resources) {\n\t\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\t\tthis.pathMetadata.set(r.path, r.metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn resources.filter((r) => r.enabled);\n\t\t};\n\n\t\tconst getEnabledPaths = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): string[] => getEnabledResources(resources).map((r) => r.path);\n\n\t\t// Store metadata and get enabled paths\n\t\tthis.pathMetadata = new Map();\n\t\tconst enabledExtensions = getEnabledPaths(resolvedPaths.extensions);\n\t\tconst enabledSkillResources = getEnabledResources(resolvedPaths.skills);\n\t\tconst enabledPrompts = getEnabledPaths(resolvedPaths.prompts);\n\t\tconst enabledThemes = getEnabledPaths(resolvedPaths.themes);\n\n\t\tconst mapSkillPath = (resource: { path: string; metadata: PathMetadata }): string => {\n\t\t\tif (resource.metadata.source !== \"auto\" && resource.metadata.origin !== \"package\") {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resource.path);\n\t\t\t\tif (!stats.isDirectory()) {\n\t\t\t\t\treturn resource.path;\n\t\t\t\t}\n\t\t\t} catch {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\tconst skillFile = join(resource.path, \"SKILL.md\");\n\t\t\tif (existsSync(skillFile)) {\n\t\t\t\tif (!this.pathMetadata.has(skillFile)) {\n\t\t\t\t\tthis.pathMetadata.set(skillFile, resource.metadata);\n\t\t\t\t}\n\t\t\t\treturn skillFile;\n\t\t\t}\n\t\t\treturn resource.path;\n\t\t};\n\n\t\tconst enabledSkills = enabledSkillResources.map(mapSkillPath);\n\n\t\t// Add CLI paths metadata\n\t\tfor (const r of cliExtensionPaths.extensions) {\n\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\tthis.pathMetadata.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\t\tfor (const r of cliExtensionPaths.skills) {\n\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\tthis.pathMetadata.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\n\t\tconst cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);\n\t\tconst cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);\n\t\tconst cliEnabledPrompts = getEnabledPaths(cliExtensionPaths.prompts);\n\t\tconst cliEnabledThemes = getEnabledPaths(cliExtensionPaths.themes);\n\n\t\tconst extensionPaths = this.noExtensions\n\t\t\t? cliEnabledExtensions\n\t\t\t: this.mergePaths(enabledExtensions, cliEnabledExtensions);\n\n\t\tconst extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);\n\t\tconst inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);\n\t\textensionsResult.extensions.push(...inlineExtensions.extensions);\n\t\textensionsResult.errors.push(...inlineExtensions.errors);\n\n\t\t// Detect extension conflicts (tools, commands, flags with same names from different extensions)\n\t\t// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.\n\t\tconst conflicts = this.detectExtensionConflicts(extensionsResult.extensions);\n\t\tfor (const conflict of conflicts) {\n\t\t\textensionsResult.errors.push({ path: conflict.path, error: conflict.message });\n\t\t}\n\n\t\tthis.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;\n\n\t\tconst skillPaths = this.noSkills\n\t\t\t? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)\n\t\t\t: this.mergePaths([...enabledSkills, ...cliEnabledSkills], this.additionalSkillPaths);\n\n\t\tthis.lastSkillPaths = skillPaths;\n\t\tthis.updateSkillsFromPaths(skillPaths);\n\n\t\tconst promptPaths = this.noPromptTemplates\n\t\t\t? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)\n\t\t\t: this.mergePaths([...enabledPrompts, ...cliEnabledPrompts], this.additionalPromptTemplatePaths);\n\n\t\tthis.lastPromptPaths = promptPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths);\n\n\t\tconst themePaths = this.noThemes\n\t\t\t? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)\n\t\t\t: this.mergePaths([...enabledThemes, ...cliEnabledThemes], this.additionalThemePaths);\n\n\t\tthis.lastThemePaths = themePaths;\n\t\tthis.updateThemesFromPaths(themePaths);\n\n\t\tfor (const extension of this.extensionsResult.extensions) {\n\t\t\tthis.addDefaultMetadataForPath(extension.path);\n\t\t}\n\n\t\tconst agentsFiles = {\n\t\t\tagentsFiles: loadProjectContextFiles({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\thomeDir: this.homeDir,\n\t\t\t\torganizationDir: this.organizationDir,\n\t\t\t\tcontextProfile: this.contextProfile,\n\t\t\t}),\n\t\t};\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\n\t\tconst baseSystemPrompt = resolvePromptInput(\n\t\t\tthis.systemPromptSource ?? this.discoverSystemPromptFile(),\n\t\t\t\"system prompt\",\n\t\t);\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst appendSource = this.appendSystemPromptSource ?? this.discoverAppendSystemPromptFile();\n\t\tconst resolvedAppend = resolvePromptInput(appendSource, \"append system prompt\");\n\t\tconst baseAppend = resolvedAppend ? [resolvedAppend] : [];\n\t\tthis.appendSystemPrompt = this.appendSystemPromptOverride\n\t\t\t? this.appendSystemPromptOverride(baseAppend)\n\t\t\t: baseAppend;\n\n\t\tthis.hooks = loadHooksConfig({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\thomeDir: this.homeDir,\n\t\t\torganizationDir: this.organizationDir,\n\t\t});\n\t}\n\n\tprivate normalizeExtensionPaths(\n\t\tentries: Array<{ path: string; metadata: PathMetadata }>,\n\t): Array<{ path: string; metadata: PathMetadata }> {\n\t\treturn entries.map((entry) => ({\n\t\t\tpath: this.resolveResourcePath(entry.path),\n\t\t\tmetadata: entry.metadata,\n\t\t}));\n\t}\n\n\tprivate updateSkillsFromPaths(\n\t\tskillPaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet skillsResult: { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noSkills && skillPaths.length === 0) {\n\t\t\tskillsResult = { skills: [], diagnostics: [] };\n\t\t} else {\n\t\t\tskillsResult = loadSkills({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tskillPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t}\n\t\tconst resolvedSkills = this.skillsOverride ? this.skillsOverride(skillsResult) : skillsResult;\n\t\tthis.skills = resolvedSkills.skills;\n\t\tthis.skillDiagnostics = resolvedSkills.diagnostics;\n\t\tthis.applyExtensionMetadata(\n\t\t\textensionPaths,\n\t\t\tthis.skills.map((skill) => skill.filePath),\n\t\t);\n\t\tfor (const skill of this.skills) {\n\t\t\tthis.addDefaultMetadataForPath(skill.filePath);\n\t\t}\n\t}\n\n\tprivate updatePromptsFromPaths(\n\t\tpromptPaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noPromptTemplates && promptPaths.length === 0) {\n\t\t\tpromptsResult = { prompts: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst allPrompts = loadPromptTemplates({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tpromptPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t\tpromptsResult = this.dedupePrompts(allPrompts);\n\t\t}\n\t\tconst resolvedPrompts = this.promptsOverride ? this.promptsOverride(promptsResult) : promptsResult;\n\t\tthis.prompts = resolvedPrompts.prompts;\n\t\tthis.promptDiagnostics = resolvedPrompts.diagnostics;\n\t\tthis.applyExtensionMetadata(\n\t\t\textensionPaths,\n\t\t\tthis.prompts.map((prompt) => prompt.filePath),\n\t\t);\n\t\tfor (const prompt of this.prompts) {\n\t\t\tthis.addDefaultMetadataForPath(prompt.filePath);\n\t\t}\n\t}\n\n\tprivate updateThemesFromPaths(\n\t\tthemePaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet themesResult: { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noThemes && themePaths.length === 0) {\n\t\t\tthemesResult = { themes: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst loaded = this.loadThemes(themePaths, false);\n\t\t\tconst deduped = this.dedupeThemes(loaded.themes);\n\t\t\tthemesResult = { themes: deduped.themes, diagnostics: [...loaded.diagnostics, ...deduped.diagnostics] };\n\t\t}\n\t\tconst resolvedThemes = this.themesOverride ? this.themesOverride(themesResult) : themesResult;\n\t\tthis.themes = resolvedThemes.themes;\n\t\tthis.themeDiagnostics = resolvedThemes.diagnostics;\n\t\tconst themePathsWithSource = this.themes.flatMap((theme) => (theme.sourcePath ? [theme.sourcePath] : []));\n\t\tthis.applyExtensionMetadata(extensionPaths, themePathsWithSource);\n\t\tfor (const theme of this.themes) {\n\t\t\tif (theme.sourcePath) {\n\t\t\t\tthis.addDefaultMetadataForPath(theme.sourcePath);\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate applyExtensionMetadata(\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }>,\n\t\tresourcePaths: string[],\n\t): void {\n\t\tif (extensionPaths.length === 0) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst normalized = extensionPaths.map((entry) => ({\n\t\t\tpath: resolve(entry.path),\n\t\t\tmetadata: entry.metadata,\n\t\t}));\n\n\t\tfor (const entry of normalized) {\n\t\t\tif (!this.pathMetadata.has(entry.path)) {\n\t\t\t\tthis.pathMetadata.set(entry.path, entry.metadata);\n\t\t\t}\n\t\t}\n\n\t\tfor (const resourcePath of resourcePaths) {\n\t\t\tconst normalizedResourcePath = resolve(resourcePath);\n\t\t\tif (this.pathMetadata.has(normalizedResourcePath) || this.pathMetadata.has(resourcePath)) {\n\t\t\t\tcontinue;\n\t\t\t}\n\t\t\tconst match = normalized.find(\n\t\t\t\t(entry) =>\n\t\t\t\t\tnormalizedResourcePath === entry.path || normalizedResourcePath.startsWith(`${entry.path}${sep}`),\n\t\t\t);\n\t\t\tif (match) {\n\t\t\t\tthis.pathMetadata.set(normalizedResourcePath, match.metadata);\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate mergePaths(primary: string[], additional: string[]): string[] {\n\t\tconst merged: string[] = [];\n\t\tconst seen = new Set<string>();\n\n\t\tfor (const p of [...primary, ...additional]) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (seen.has(resolved)) continue;\n\t\t\tseen.add(resolved);\n\t\t\tmerged.push(resolved);\n\t\t}\n\n\t\treturn merged;\n\t}\n\n\tprivate resolveResourcePath(p: string): string {\n\t\tconst trimmed = p.trim();\n\t\tlet expanded = trimmed;\n\t\tif (trimmed === \"~\") {\n\t\t\texpanded = homedir();\n\t\t} else if (trimmed.startsWith(\"~/\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(2));\n\t\t} else if (trimmed.startsWith(\"~\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(1));\n\t\t}\n\t\treturn resolve(this.cwd, expanded);\n\t}\n\n\tprivate loadThemes(\n\t\tpaths: string[],\n\t\tincludeDefaults: boolean = true,\n\t): {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t} {\n\t\tconst themes: Theme[] = [];\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\t\tif (includeDefaults) {\n\t\t\tconst defaultDirs = [join(this.agentDir, \"themes\"), join(this.cwd, CONFIG_DIR_NAME, \"themes\")];\n\n\t\t\tfor (const dir of defaultDirs) {\n\t\t\t\tthis.loadThemesFromDir(dir, themes, diagnostics);\n\t\t\t}\n\t\t}\n\n\t\tfor (const p of paths) {\n\t\t\tconst resolved = resolve(this.cwd, p);\n\t\t\tif (!existsSync(resolved)) {\n\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path does not exist\", path: resolved });\n\t\t\t\tcontinue;\n\t\t\t}\n\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resolved);\n\t\t\t\tif (stats.isDirectory()) {\n\t\t\t\t\tthis.loadThemesFromDir(resolved, themes, diagnostics);\n\t\t\t\t} else if (stats.isFile() && resolved.endsWith(\".json\")) {\n\t\t\t\t\tthis.loadThemeFromFile(resolved, themes, diagnostics);\n\t\t\t\t} else {\n\t\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path is not a json file\", path: resolved });\n\t\t\t\t}\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme path\";\n\t\t\t\tdiagnostics.push({ type: \"warning\", message, path: resolved });\n\t\t\t}\n\t\t}\n\n\t\treturn { themes, diagnostics };\n\t}\n\n\tprivate loadThemesFromDir(dir: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\tif (!existsSync(dir)) {\n\t\t\treturn;\n\t\t}\n\n\t\ttry {\n\t\t\tconst entries = readdirSync(dir, { withFileTypes: true });\n\t\t\tfor (const entry of entries) {\n\t\t\t\tlet isFile = entry.isFile();\n\t\t\t\tif (entry.isSymbolicLink()) {\n\t\t\t\t\ttry {\n\t\t\t\t\t\tisFile = statSync(join(dir, entry.name)).isFile();\n\t\t\t\t\t} catch {\n\t\t\t\t\t\tcontinue;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!isFile) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tif (!entry.name.endsWith(\".json\")) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tthis.loadThemeFromFile(join(dir, entry.name), themes, diagnostics);\n\t\t\t}\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme directory\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: dir });\n\t\t}\n\t}\n\n\tprivate loadThemeFromFile(filePath: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\ttry {\n\t\t\tthemes.push(loadThemeFromPath(filePath));\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to load theme\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: filePath });\n\t\t}\n\t}\n\n\tprivate async loadExtensionFactories(runtime: ExtensionRuntime): Promise<{\n\t\textensions: Extension[];\n\t\terrors: Array<{ path: string; error: string }>;\n\t}> {\n\t\tconst extensions: Extension[] = [];\n\t\tconst errors: Array<{ path: string; error: string }> = [];\n\n\t\tfor (const [index, factory] of this.extensionFactories.entries()) {\n\t\t\tconst extensionPath = `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(factory, this.cwd, this.eventBus, runtime, extensionPath);\n\t\t\t\textensions.push(extension);\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to load extension\";\n\t\t\t\terrors.push({ path: extensionPath, error: message });\n\t\t\t}\n\t\t}\n\n\t\treturn { extensions, errors };\n\t}\n\n\tprivate dedupePrompts(prompts: PromptTemplate[]): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, PromptTemplate>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const prompt of prompts) {\n\t\t\tconst existing = seen.get(prompt.name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"/${prompt.name}\" collision`,\n\t\t\t\t\tpath: prompt.filePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"prompt\",\n\t\t\t\t\t\tname: prompt.name,\n\t\t\t\t\t\twinnerPath: existing.filePath,\n\t\t\t\t\t\tloserPath: prompt.filePath,\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(prompt.name, prompt);\n\t\t\t}\n\t\t}\n\n\t\treturn { prompts: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate dedupeThemes(themes: Theme[]): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, Theme>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const t of themes) {\n\t\t\tconst name = t.name ?? \"unnamed\";\n\t\t\tconst existing = seen.get(name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"${name}\" collision`,\n\t\t\t\t\tpath: t.sourcePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"theme\",\n\t\t\t\t\t\tname,\n\t\t\t\t\t\twinnerPath: existing.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t\tloserPath: t.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(name, t);\n\t\t\t}\n\t\t}\n\n\t\treturn { themes: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate discoverSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate discoverAppendSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate addDefaultMetadataForPath(filePath: string): void {\n\t\tif (!filePath || filePath.startsWith(\"<\")) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst normalizedPath = resolve(filePath);\n\t\tif (this.pathMetadata.has(normalizedPath) || this.pathMetadata.has(filePath)) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst agentRoots = [\n\t\t\tjoin(this.agentDir, \"skills\"),\n\t\t\tjoin(this.agentDir, \"prompts\"),\n\t\t\tjoin(this.agentDir, \"themes\"),\n\t\t\tjoin(this.agentDir, \"extensions\"),\n\t\t];\n\t\tconst projectRoots = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"skills\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"prompts\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"themes\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"extensions\"),\n\t\t];\n\n\t\tfor (const root of agentRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\tthis.pathMetadata.set(normalizedPath, { source: \"local\", scope: \"user\", origin: \"top-level\" });\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tfor (const root of projectRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\tthis.pathMetadata.set(normalizedPath, { source: \"local\", scope: \"project\", origin: \"top-level\" });\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate isUnderPath(target: string, root: string): boolean {\n\t\tconst normalizedRoot = resolve(root);\n\t\tif (target === normalizedRoot) {\n\t\t\treturn true;\n\t\t}\n\t\tconst prefix = normalizedRoot.endsWith(sep) ? normalizedRoot : `${normalizedRoot}${sep}`;\n\t\treturn target.startsWith(prefix);\n\t}\n\n\tprivate detectExtensionConflicts(extensions: Extension[]): Array<{ path: string; message: string }> {\n\t\tconst conflicts: Array<{ path: string; message: string }> = [];\n\n\t\t// Track which extension registered each tool, command, and flag\n\t\tconst toolOwners = new Map<string, string>();\n\t\tconst commandOwners = new Map<string, string>();\n\t\tconst flagOwners = new Map<string, string>();\n\n\t\tfor (const ext of extensions) {\n\t\t\t// Check tools\n\t\t\tfor (const toolName of ext.tools.keys()) {\n\t\t\t\tconst existingOwner = toolOwners.get(toolName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Tool \"${toolName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\ttoolOwners.set(toolName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check commands\n\t\t\tfor (const commandName of ext.commands.keys()) {\n\t\t\t\tconst existingOwner = commandOwners.get(commandName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Command \"/${commandName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tcommandOwners.set(commandName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check flags\n\t\t\tfor (const flagName of ext.flags.keys()) {\n\t\t\t\tconst existingOwner = flagOwners.get(flagName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Flag \"--${flagName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tflagOwners.set(flagName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn conflicts;\n\t}\n}\n"]}
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{ existsSync, lstatSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { join, resolve, sep } from \"node:path\";\nimport chalk from \"chalk\";\nimport { CONFIG_DIR_NAME, getAgentDir } from \"../config.js\";\nimport { buildIosmContextBlock } from \"../iosm/context-loader.js\";\nimport { loadThemeFromPath, type Theme } from \"../modes/interactive/theme/theme.js\";\nimport type { ResourceDiagnostic } from \"./diagnostics.js\";\n\nexport type { ResourceCollision, ResourceDiagnostic } from \"./diagnostics.js\";\n\nimport { createEventBus, type EventBus } from \"./event-bus.js\";\nimport { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from \"./extensions/loader.js\";\nimport type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from \"./extensions/types.js\";\nimport { DefaultPackageManager, type PathMetadata } from \"./package-manager.js\";\nimport type { PromptTemplate } from 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content: string }> };\n\tgetSystemPrompt(): string | undefined;\n\tgetAppendSystemPrompt(): string[];\n\tgetHooks?(): LoadedHooksConfig;\n\tgetPathMetadata(): Map<string, PathMetadata>;\n\textendResources(paths: ResourceExtensionPaths): void;\n\treload(): Promise<void>;\n}\n\nfunction resolvePromptInput(input: string | undefined, description: string): string | undefined {\n\tif (!input) {\n\t\treturn undefined;\n\t}\n\n\tif (existsSync(input)) {\n\t\ttry {\n\t\t\treturn readFileSync(input, \"utf-8\");\n\t\t} catch (error) {\n\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${description} file ${input}: ${error}`));\n\t\t\treturn input;\n\t\t}\n\t}\n\n\treturn input;\n}\n\nfunction normalizeContextProfile(profile: string | undefined): ContextProfile {\n\treturn profile?.toLowerCase() === \"iosm\" ? \"iosm\" : \"standard\";\n}\n\nfunction expandHomePath(pathValue: string, homeDir: string): string {\n\tif (pathValue === \"~\") return homeDir;\n\tif (pathValue.startsWith(\"~/\")) 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[\"AGENTS.md\"] : []),\n\t\t...(includeIosm ? 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content: string }> {\n\tconst result: Array<{ path: string; content: string }> = [];\n\tconst memoryRootFile = join(configDir, \"memory.md\");\n\tconst expandedRoot = loadExpandedMemoryFile(memoryRootFile);\n\tif (expandedRoot && expandedRoot.trim().length > 0) {\n\t\tresult.push({ path: memoryRootFile, content: expandedRoot });\n\t}\n\n\tconst memoryDir = join(configDir, \"memory\");\n\tif (!existsSync(memoryDir)) return result;\n\tfor (const filePath of listMarkdownFilesRecursive(memoryDir)) {\n\t\tconst expanded = loadExpandedMemoryFile(filePath);\n\t\tif (!expanded || expanded.trim().length === 0) continue;\n\t\tresult.push({ path: filePath, content: expanded });\n\t}\n\n\treturn result;\n}\n\nfunction loadMemoryContextFilesFromRoot(rootDir: string): Array<{ path: string; content: string }> {\n\treturn loadMemoryContextFilesFromConfigDir(join(rootDir, \".iosm\"));\n}\n\nfunction loadMemoryContextFilesFromAgentDir(agentDir: string): Array<{ path: string; content: string }> {\n\tconst files: Array<{ path: string; content: string }> = [];\n\tconst seen = new Set<string>();\n\tconst addUnique = (entry: { path: string; content: string }) => {\n\t\tconst resolvedPath = resolve(entry.path);\n\t\tif (seen.has(resolvedPath)) return;\n\t\tseen.add(resolvedPath);\n\t\tfiles.push(entry);\n\t};\n\n\tfor (const entry of loadMemoryContextFilesFromConfigDir(agentDir)) addUnique(entry);\n\tfor (const entry of loadMemoryContextFilesFromRoot(agentDir)) addUnique(entry);\n\treturn files;\n}\n\nfunction loadProjectContextFiles(\n\toptions: {\n\t\tcwd?: string;\n\t\tagentDir?: string;\n\t\thomeDir?: string;\n\t\torganizationDir?: string;\n\t\tcontextProfile?: ContextProfile | string;\n\t} = {},\n): Array<{ path: string; content: string }> {\n\tconst resolvedCwd = options.cwd ?? process.cwd();\n\tconst resolvedAgentDir = options.agentDir ?? getAgentDir();\n\tconst resolvedHomeDir = options.homeDir ?? homedir();\n\t// Keep IOSM context files loaded regardless of startup profile.\n\t// The active profile still controls what is injected into prompts and shown in UI.\n\t// This prevents context loss when operators switch profile at runtime.\n\tconst includeIosm = true;\n\tconst organizationDirEnv = options.organizationDir ?? process.env.IOSM_ORG_DIR ?? process.env.PI_ORG_DIR;\n\tconst resolvedOrganizationDir = organizationDirEnv\n\t\t? resolve(expandHomePath(organizationDirEnv, resolvedHomeDir))\n\t\t: undefined;\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst seenPaths = new Set<string>();\n\tconst appendUnique = (entry: { path: string; content: string }) => {\n\t\tif (seenPaths.has(entry.path)) return;\n\t\tcontextFiles.push(entry);\n\t\tseenPaths.add(entry.path);\n\t};\n\n\tif (resolvedOrganizationDir) {\n\t\tfor (const organizationContext of loadContextFilesFromDir(resolvedOrganizationDir, { includeIosm })) {\n\t\t\tappendUnique(organizationContext);\n\t\t}\n\t\tfor (const organizationMemory of loadMemoryContextFilesFromRoot(resolvedOrganizationDir)) {\n\t\t\tappendUnique(organizationMemory);\n\t\t}\n\t}\n\n\tconst userConfigDir = join(resolvedHomeDir, \".iosm\");\n\tfor (const userContext of loadContextFilesFromDir(userConfigDir, { includeIosm })) {\n\t\tappendUnique(userContext);\n\t}\n\tfor (const userMemory of loadMemoryContextFilesFromRoot(resolvedHomeDir)) {\n\t\tappendUnique(userMemory);\n\t}\n\n\tfor (const globalContext of loadContextFilesFromDir(resolvedAgentDir, { includeIosm })) {\n\t\tappendUnique(globalContext);\n\t}\n\tfor (const globalMemory of loadMemoryContextFilesFromAgentDir(resolvedAgentDir)) {\n\t\tappendUnique(globalMemory);\n\t}\n\n\tconst ancestorContextFiles: Array<{ path: string; content: string }> = [];\n\n\tlet currentDir = resolvedCwd;\n\tconst root = resolve(\"/\");\n\n\twhile (true) {\n\t\tconst contextFilesInDir = loadContextFilesFromDir(currentDir, { includeIosm });\n\t\tfor (let index = contextFilesInDir.length - 1; index >= 0; index--) {\n\t\t\tconst contextFile = contextFilesInDir[index];\n\t\t\tif (seenPaths.has(contextFile.path)) {\n\t\t\t\tcontinue;\n\t\t\t}\n\t\t\tancestorContextFiles.unshift(contextFile);\n\t\t\tseenPaths.add(contextFile.path);\n\t\t}\n\t\tconst memoryFilesInDir = loadMemoryContextFilesFromRoot(currentDir);\n\t\tfor (let index = memoryFilesInDir.length - 1; index >= 0; index--) {\n\t\t\tconst memoryFile = memoryFilesInDir[index];\n\t\t\tif (seenPaths.has(memoryFile.path)) continue;\n\t\t\tancestorContextFiles.unshift(memoryFile);\n\t\t\tseenPaths.add(memoryFile.path);\n\t\t}\n\n\t\tif (currentDir === root) break;\n\n\t\tconst parentDir = resolve(currentDir, \"..\");\n\t\tif (parentDir === currentDir) break;\n\t\tcurrentDir = parentDir;\n\t}\n\n\tcontextFiles.push(...ancestorContextFiles);\n\n\treturn contextFiles;\n}\n\nexport interface DefaultResourceLoaderOptions {\n\tcwd?: string;\n\tagentDir?: string;\n\thomeDir?: string;\n\torganizationDir?: string;\n\tcontextProfile?: ContextProfile | string;\n\tsettingsManager?: SettingsManager;\n\teventBus?: EventBus;\n\tadditionalExtensionPaths?: string[];\n\tadditionalSkillPaths?: string[];\n\tadditionalPromptTemplatePaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoThemes?: boolean;\n\tsystemPrompt?: string;\n\tappendSystemPrompt?: string;\n\textensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tskillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tpromptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tthemesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tagentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tsystemPromptOverride?: (base: string | undefined) => string | undefined;\n\tappendSystemPromptOverride?: (base: string[]) => string[];\n}\n\nexport class DefaultResourceLoader implements ResourceLoader {\n\tprivate cwd: string;\n\tprivate agentDir: string;\n\tprivate homeDir: string;\n\tprivate organizationDir?: string;\n\tprivate contextProfile: ContextProfile;\n\tprivate settingsManager: SettingsManager;\n\tprivate eventBus: EventBus;\n\tprivate packageManager: DefaultPackageManager;\n\tprivate additionalExtensionPaths: string[];\n\tprivate additionalSkillPaths: string[];\n\tprivate additionalPromptTemplatePaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noThemes: boolean;\n\tprivate systemPromptSource?: string;\n\tprivate appendSystemPromptSource?: string;\n\tprivate extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tprivate skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tprivate systemPromptOverride?: (base: string | undefined) => string | undefined;\n\tprivate appendSystemPromptOverride?: (base: string[]) => string[];\n\n\tprivate extensionsResult: LoadExtensionsResult;\n\tprivate skills: Skill[];\n\tprivate skillDiagnostics: ResourceDiagnostic[];\n\tprivate prompts: PromptTemplate[];\n\tprivate promptDiagnostics: ResourceDiagnostic[];\n\tprivate themes: Theme[];\n\tprivate themeDiagnostics: ResourceDiagnostic[];\n\tprivate agentsFiles: Array<{ path: string; content: string }>;\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate hooks: LoadedHooksConfig;\n\tprivate pathMetadata: Map<string, PathMetadata>;\n\tprivate lastSkillPaths: string[];\n\tprivate lastPromptPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = options.cwd ?? process.cwd();\n\t\tthis.agentDir = options.agentDir ?? getAgentDir();\n\t\tthis.homeDir = options.homeDir ?? homedir();\n\t\tthis.organizationDir = options.organizationDir;\n\t\tthis.contextProfile = normalizeContextProfile(options.contextProfile);\n\t\tthis.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);\n\t\tthis.eventBus = options.eventBus ?? createEventBus();\n\t\tthis.packageManager = new DefaultPackageManager({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\tsettingsManager: this.settingsManager,\n\t\t});\n\t\tthis.additionalExtensionPaths = options.additionalExtensionPaths ?? [];\n\t\tthis.additionalSkillPaths = options.additionalSkillPaths ?? [];\n\t\tthis.additionalPromptTemplatePaths = options.additionalPromptTemplatePaths ?? [];\n\t\tthis.additionalThemePaths = options.additionalThemePaths ?? [];\n\t\tthis.extensionFactories = options.extensionFactories ?? [];\n\t\tthis.noExtensions = options.noExtensions ?? false;\n\t\tthis.noSkills = options.noSkills ?? false;\n\t\tthis.noPromptTemplates = options.noPromptTemplates ?? false;\n\t\tthis.noThemes = options.noThemes ?? false;\n\t\tthis.systemPromptSource = options.systemPrompt;\n\t\tthis.appendSystemPromptSource = options.appendSystemPrompt;\n\t\tthis.extensionsOverride = options.extensionsOverride;\n\t\tthis.skillsOverride = options.skillsOverride;\n\t\tthis.promptsOverride = options.promptsOverride;\n\t\tthis.themesOverride = options.themesOverride;\n\t\tthis.agentsFilesOverride = options.agentsFilesOverride;\n\t\tthis.systemPromptOverride = options.systemPromptOverride;\n\t\tthis.appendSystemPromptOverride = options.appendSystemPromptOverride;\n\n\t\tthis.extensionsResult = { extensions: [], errors: [], runtime: createExtensionRuntime() };\n\t\tthis.skills = [];\n\t\tthis.skillDiagnostics = [];\n\t\tthis.prompts = [];\n\t\tthis.promptDiagnostics = [];\n\t\tthis.themes = [];\n\t\tthis.themeDiagnostics = [];\n\t\tthis.agentsFiles = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.hooks = emptyHooksConfig();\n\t\tthis.pathMetadata = new Map();\n\t\tthis.lastSkillPaths = [];\n\t\tthis.lastPromptPaths = [];\n\t\tthis.lastThemePaths = [];\n\t}\n\n\tgetExtensions(): LoadExtensionsResult {\n\t\treturn this.extensionsResult;\n\t}\n\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { skills: this.skills, diagnostics: this.skillDiagnostics };\n\t}\n\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { prompts: this.prompts, diagnostics: this.promptDiagnostics };\n\t}\n\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { themes: this.themes, diagnostics: this.themeDiagnostics };\n\t}\n\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> } {\n\t\treturn { agentsFiles: this.agentsFiles };\n\t}\n\n\tgetSystemPrompt(): string | undefined {\n\t\treturn this.systemPrompt;\n\t}\n\n\tgetAppendSystemPrompt(): string[] {\n\t\treturn this.appendSystemPrompt;\n\t}\n\n\tgetHooks(): LoadedHooksConfig {\n\t\treturn this.hooks;\n\t}\n\n\tgetPathMetadata(): Map<string, PathMetadata> {\n\t\treturn this.pathMetadata;\n\t}\n\n\textendResources(paths: ResourceExtensionPaths): void {\n\t\tconst skillPaths = this.normalizeExtensionPaths(paths.skillPaths ?? []);\n\t\tconst promptPaths = this.normalizeExtensionPaths(paths.promptPaths ?? []);\n\t\tconst themePaths = this.normalizeExtensionPaths(paths.themePaths ?? []);\n\n\t\tif (skillPaths.length > 0) {\n\t\t\tthis.lastSkillPaths = this.mergePaths(\n\t\t\t\tthis.lastSkillPaths,\n\t\t\t\tskillPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateSkillsFromPaths(this.lastSkillPaths, skillPaths);\n\t\t}\n\n\t\tif (promptPaths.length > 0) {\n\t\t\tthis.lastPromptPaths = this.mergePaths(\n\t\t\t\tthis.lastPromptPaths,\n\t\t\t\tpromptPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updatePromptsFromPaths(this.lastPromptPaths, promptPaths);\n\t\t}\n\n\t\tif (themePaths.length > 0) {\n\t\t\tthis.lastThemePaths = this.mergePaths(\n\t\t\t\tthis.lastThemePaths,\n\t\t\t\tthemePaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateThemesFromPaths(this.lastThemePaths, themePaths);\n\t\t}\n\t}\n\n\tasync reload(): Promise<void> {\n\t\tconst resolvedPaths = await this.packageManager.resolve();\n\t\tconst cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {\n\t\t\ttemporary: true,\n\t\t});\n\n\t\t// Helper to extract enabled paths and store metadata\n\t\tconst getEnabledResources = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): Array<{ path: string; enabled: boolean; metadata: PathMetadata }> => {\n\t\t\tfor (const r of resources) {\n\t\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\t\tthis.pathMetadata.set(r.path, r.metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn resources.filter((r) => r.enabled);\n\t\t};\n\n\t\tconst getEnabledPaths = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): string[] => getEnabledResources(resources).map((r) => r.path);\n\n\t\t// Store metadata and get enabled paths\n\t\tthis.pathMetadata = new Map();\n\t\tconst enabledExtensions = getEnabledPaths(resolvedPaths.extensions);\n\t\tconst enabledSkillResources = getEnabledResources(resolvedPaths.skills);\n\t\tconst enabledPrompts = getEnabledPaths(resolvedPaths.prompts);\n\t\tconst enabledThemes = getEnabledPaths(resolvedPaths.themes);\n\n\t\tconst mapSkillPath = (resource: { path: string; metadata: PathMetadata }): string => {\n\t\t\tif (resource.metadata.source !== \"auto\" && resource.metadata.origin !== \"package\") {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resource.path);\n\t\t\t\tif (!stats.isDirectory()) {\n\t\t\t\t\treturn resource.path;\n\t\t\t\t}\n\t\t\t} catch {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\tconst skillFile = join(resource.path, \"SKILL.md\");\n\t\t\tif (existsSync(skillFile)) {\n\t\t\t\tif (!this.pathMetadata.has(skillFile)) {\n\t\t\t\t\tthis.pathMetadata.set(skillFile, resource.metadata);\n\t\t\t\t}\n\t\t\t\treturn skillFile;\n\t\t\t}\n\t\t\treturn resource.path;\n\t\t};\n\n\t\tconst enabledSkills = enabledSkillResources.map(mapSkillPath);\n\n\t\t// Add CLI paths metadata\n\t\tfor (const r of cliExtensionPaths.extensions) {\n\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\tthis.pathMetadata.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\t\tfor (const r of cliExtensionPaths.skills) {\n\t\t\tif (!this.pathMetadata.has(r.path)) {\n\t\t\t\tthis.pathMetadata.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\n\t\tconst cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);\n\t\tconst cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);\n\t\tconst cliEnabledPrompts = getEnabledPaths(cliExtensionPaths.prompts);\n\t\tconst cliEnabledThemes = getEnabledPaths(cliExtensionPaths.themes);\n\n\t\tconst extensionPaths = this.noExtensions\n\t\t\t? cliEnabledExtensions\n\t\t\t: this.mergePaths(enabledExtensions, cliEnabledExtensions);\n\n\t\tconst extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);\n\t\tconst inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);\n\t\textensionsResult.extensions.push(...inlineExtensions.extensions);\n\t\textensionsResult.errors.push(...inlineExtensions.errors);\n\n\t\t// Detect extension conflicts (tools, commands, flags with same names from different extensions)\n\t\t// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.\n\t\tconst conflicts = this.detectExtensionConflicts(extensionsResult.extensions);\n\t\tfor (const conflict of conflicts) {\n\t\t\textensionsResult.errors.push({ path: conflict.path, error: conflict.message });\n\t\t}\n\n\t\tthis.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;\n\n\t\tconst skillPaths = this.noSkills\n\t\t\t? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)\n\t\t\t: this.mergePaths([...enabledSkills, ...cliEnabledSkills], this.additionalSkillPaths);\n\n\t\tthis.lastSkillPaths = skillPaths;\n\t\tthis.updateSkillsFromPaths(skillPaths);\n\n\t\tconst promptPaths = this.noPromptTemplates\n\t\t\t? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)\n\t\t\t: this.mergePaths([...enabledPrompts, ...cliEnabledPrompts], this.additionalPromptTemplatePaths);\n\n\t\tthis.lastPromptPaths = promptPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths);\n\n\t\tconst themePaths = this.noThemes\n\t\t\t? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)\n\t\t\t: this.mergePaths([...enabledThemes, ...cliEnabledThemes], this.additionalThemePaths);\n\n\t\tthis.lastThemePaths = themePaths;\n\t\tthis.updateThemesFromPaths(themePaths);\n\n\t\tfor (const extension of this.extensionsResult.extensions) {\n\t\t\tthis.addDefaultMetadataForPath(extension.path);\n\t\t}\n\n\t\tconst agentsFiles = {\n\t\t\tagentsFiles: loadProjectContextFiles({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\thomeDir: this.homeDir,\n\t\t\t\torganizationDir: this.organizationDir,\n\t\t\t\tcontextProfile: this.contextProfile,\n\t\t\t}),\n\t\t};\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\n\t\tconst baseSystemPrompt = resolvePromptInput(\n\t\t\tthis.systemPromptSource ?? this.discoverSystemPromptFile(),\n\t\t\t\"system prompt\",\n\t\t);\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst appendSource = this.appendSystemPromptSource ?? this.discoverAppendSystemPromptFile();\n\t\tconst resolvedAppend = resolvePromptInput(appendSource, \"append system prompt\");\n\t\tconst baseAppend = resolvedAppend ? [resolvedAppend] : [];\n\t\tthis.appendSystemPrompt = this.appendSystemPromptOverride\n\t\t\t? this.appendSystemPromptOverride(baseAppend)\n\t\t\t: baseAppend;\n\n\t\tthis.hooks = loadHooksConfig({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\thomeDir: this.homeDir,\n\t\t\torganizationDir: this.organizationDir,\n\t\t});\n\t}\n\n\tprivate normalizeExtensionPaths(\n\t\tentries: Array<{ path: string; metadata: PathMetadata }>,\n\t): Array<{ path: string; metadata: PathMetadata }> {\n\t\treturn entries.map((entry) => ({\n\t\t\tpath: this.resolveResourcePath(entry.path),\n\t\t\tmetadata: entry.metadata,\n\t\t}));\n\t}\n\n\tprivate updateSkillsFromPaths(\n\t\tskillPaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet skillsResult: { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noSkills && skillPaths.length === 0) {\n\t\t\tskillsResult = { skills: [], diagnostics: [] };\n\t\t} else {\n\t\t\tskillsResult = loadSkills({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tskillPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t}\n\t\tconst resolvedSkills = this.skillsOverride ? this.skillsOverride(skillsResult) : skillsResult;\n\t\tthis.skills = resolvedSkills.skills;\n\t\tthis.skillDiagnostics = resolvedSkills.diagnostics;\n\t\tthis.applyExtensionMetadata(\n\t\t\textensionPaths,\n\t\t\tthis.skills.map((skill) => skill.filePath),\n\t\t);\n\t\tfor (const skill of this.skills) {\n\t\t\tthis.addDefaultMetadataForPath(skill.filePath);\n\t\t}\n\t}\n\n\tprivate updatePromptsFromPaths(\n\t\tpromptPaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noPromptTemplates && promptPaths.length === 0) {\n\t\t\tpromptsResult = { prompts: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst allPrompts = loadPromptTemplates({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tpromptPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t\tpromptsResult = this.dedupePrompts(allPrompts);\n\t\t}\n\t\tconst resolvedPrompts = this.promptsOverride ? this.promptsOverride(promptsResult) : promptsResult;\n\t\tthis.prompts = resolvedPrompts.prompts;\n\t\tthis.promptDiagnostics = resolvedPrompts.diagnostics;\n\t\tthis.applyExtensionMetadata(\n\t\t\textensionPaths,\n\t\t\tthis.prompts.map((prompt) => prompt.filePath),\n\t\t);\n\t\tfor (const prompt of this.prompts) {\n\t\t\tthis.addDefaultMetadataForPath(prompt.filePath);\n\t\t}\n\t}\n\n\tprivate updateThemesFromPaths(\n\t\tthemePaths: string[],\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }> = [],\n\t): void {\n\t\tlet themesResult: { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noThemes && themePaths.length === 0) {\n\t\t\tthemesResult = { themes: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst loaded = this.loadThemes(themePaths, false);\n\t\t\tconst deduped = this.dedupeThemes(loaded.themes);\n\t\t\tthemesResult = { themes: deduped.themes, diagnostics: [...loaded.diagnostics, ...deduped.diagnostics] };\n\t\t}\n\t\tconst resolvedThemes = this.themesOverride ? this.themesOverride(themesResult) : themesResult;\n\t\tthis.themes = resolvedThemes.themes;\n\t\tthis.themeDiagnostics = resolvedThemes.diagnostics;\n\t\tconst themePathsWithSource = this.themes.flatMap((theme) => (theme.sourcePath ? [theme.sourcePath] : []));\n\t\tthis.applyExtensionMetadata(extensionPaths, themePathsWithSource);\n\t\tfor (const theme of this.themes) {\n\t\t\tif (theme.sourcePath) {\n\t\t\t\tthis.addDefaultMetadataForPath(theme.sourcePath);\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate applyExtensionMetadata(\n\t\textensionPaths: Array<{ path: string; metadata: PathMetadata }>,\n\t\tresourcePaths: string[],\n\t): void {\n\t\tif (extensionPaths.length === 0) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst normalized = extensionPaths.map((entry) => ({\n\t\t\tpath: resolve(entry.path),\n\t\t\tmetadata: entry.metadata,\n\t\t}));\n\n\t\tfor (const entry of normalized) {\n\t\t\tif (!this.pathMetadata.has(entry.path)) {\n\t\t\t\tthis.pathMetadata.set(entry.path, entry.metadata);\n\t\t\t}\n\t\t}\n\n\t\tfor (const resourcePath of resourcePaths) {\n\t\t\tconst normalizedResourcePath = resolve(resourcePath);\n\t\t\tif (this.pathMetadata.has(normalizedResourcePath) || this.pathMetadata.has(resourcePath)) {\n\t\t\t\tcontinue;\n\t\t\t}\n\t\t\tconst match = normalized.find(\n\t\t\t\t(entry) =>\n\t\t\t\t\tnormalizedResourcePath === entry.path || normalizedResourcePath.startsWith(`${entry.path}${sep}`),\n\t\t\t);\n\t\t\tif (match) {\n\t\t\t\tthis.pathMetadata.set(normalizedResourcePath, match.metadata);\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate mergePaths(primary: string[], additional: string[]): string[] {\n\t\tconst merged: string[] = [];\n\t\tconst seen = new Set<string>();\n\n\t\tfor (const p of [...primary, ...additional]) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (seen.has(resolved)) continue;\n\t\t\tseen.add(resolved);\n\t\t\tmerged.push(resolved);\n\t\t}\n\n\t\treturn merged;\n\t}\n\n\tprivate resolveResourcePath(p: string): string {\n\t\tconst trimmed = p.trim();\n\t\tlet expanded = trimmed;\n\t\tif (trimmed === \"~\") {\n\t\t\texpanded = homedir();\n\t\t} else if (trimmed.startsWith(\"~/\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(2));\n\t\t} else if (trimmed.startsWith(\"~\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(1));\n\t\t}\n\t\treturn resolve(this.cwd, expanded);\n\t}\n\n\tprivate loadThemes(\n\t\tpaths: string[],\n\t\tincludeDefaults: boolean = true,\n\t): {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t} {\n\t\tconst themes: Theme[] = [];\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\t\tif (includeDefaults) {\n\t\t\tconst defaultDirs = [join(this.agentDir, \"themes\"), join(this.cwd, CONFIG_DIR_NAME, \"themes\")];\n\n\t\t\tfor (const dir of defaultDirs) {\n\t\t\t\tthis.loadThemesFromDir(dir, themes, diagnostics);\n\t\t\t}\n\t\t}\n\n\t\tfor (const p of paths) {\n\t\t\tconst resolved = resolve(this.cwd, p);\n\t\t\tif (!existsSync(resolved)) {\n\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path does not exist\", path: resolved });\n\t\t\t\tcontinue;\n\t\t\t}\n\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resolved);\n\t\t\t\tif (stats.isDirectory()) {\n\t\t\t\t\tthis.loadThemesFromDir(resolved, themes, diagnostics);\n\t\t\t\t} else if (stats.isFile() && resolved.endsWith(\".json\")) {\n\t\t\t\t\tthis.loadThemeFromFile(resolved, themes, diagnostics);\n\t\t\t\t} else {\n\t\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path is not a json file\", path: resolved });\n\t\t\t\t}\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme path\";\n\t\t\t\tdiagnostics.push({ type: \"warning\", message, path: resolved });\n\t\t\t}\n\t\t}\n\n\t\treturn { themes, diagnostics };\n\t}\n\n\tprivate loadThemesFromDir(dir: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\tif (!existsSync(dir)) {\n\t\t\treturn;\n\t\t}\n\n\t\ttry {\n\t\t\tconst entries = readdirSync(dir, { withFileTypes: true });\n\t\t\tfor (const entry of entries) {\n\t\t\t\tlet isFile = entry.isFile();\n\t\t\t\tif (entry.isSymbolicLink()) {\n\t\t\t\t\ttry {\n\t\t\t\t\t\tisFile = statSync(join(dir, entry.name)).isFile();\n\t\t\t\t\t} catch {\n\t\t\t\t\t\tcontinue;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!isFile) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tif (!entry.name.endsWith(\".json\")) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tthis.loadThemeFromFile(join(dir, entry.name), themes, diagnostics);\n\t\t\t}\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme directory\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: dir });\n\t\t}\n\t}\n\n\tprivate loadThemeFromFile(filePath: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\ttry {\n\t\t\tthemes.push(loadThemeFromPath(filePath));\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to load theme\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: filePath });\n\t\t}\n\t}\n\n\tprivate async loadExtensionFactories(runtime: ExtensionRuntime): Promise<{\n\t\textensions: Extension[];\n\t\terrors: Array<{ path: string; error: string }>;\n\t}> {\n\t\tconst extensions: Extension[] = [];\n\t\tconst errors: Array<{ path: string; error: string }> = [];\n\n\t\tfor (const [index, factory] of this.extensionFactories.entries()) {\n\t\t\tconst extensionPath = `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(factory, this.cwd, this.eventBus, runtime, extensionPath);\n\t\t\t\textensions.push(extension);\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to load extension\";\n\t\t\t\terrors.push({ path: extensionPath, error: message });\n\t\t\t}\n\t\t}\n\n\t\treturn { extensions, errors };\n\t}\n\n\tprivate dedupePrompts(prompts: PromptTemplate[]): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, PromptTemplate>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const prompt of prompts) {\n\t\t\tconst existing = seen.get(prompt.name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"/${prompt.name}\" collision`,\n\t\t\t\t\tpath: prompt.filePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"prompt\",\n\t\t\t\t\t\tname: prompt.name,\n\t\t\t\t\t\twinnerPath: existing.filePath,\n\t\t\t\t\t\tloserPath: prompt.filePath,\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(prompt.name, prompt);\n\t\t\t}\n\t\t}\n\n\t\treturn { prompts: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate dedupeThemes(themes: Theme[]): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, Theme>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const t of themes) {\n\t\t\tconst name = t.name ?? \"unnamed\";\n\t\t\tconst existing = seen.get(name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"${name}\" collision`,\n\t\t\t\t\tpath: t.sourcePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"theme\",\n\t\t\t\t\t\tname,\n\t\t\t\t\t\twinnerPath: existing.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t\tloserPath: t.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(name, t);\n\t\t\t}\n\t\t}\n\n\t\treturn { themes: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate discoverSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate discoverAppendSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate addDefaultMetadataForPath(filePath: string): void {\n\t\tif (!filePath || filePath.startsWith(\"<\")) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst normalizedPath = resolve(filePath);\n\t\tif (this.pathMetadata.has(normalizedPath) || this.pathMetadata.has(filePath)) {\n\t\t\treturn;\n\t\t}\n\n\t\tconst agentRoots = [\n\t\t\tjoin(this.agentDir, \"skills\"),\n\t\t\tjoin(this.agentDir, \"prompts\"),\n\t\t\tjoin(this.agentDir, \"themes\"),\n\t\t\tjoin(this.agentDir, \"extensions\"),\n\t\t];\n\t\tconst projectRoots = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"skills\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"prompts\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"themes\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"extensions\"),\n\t\t];\n\n\t\tfor (const root of agentRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\tthis.pathMetadata.set(normalizedPath, { source: \"local\", scope: \"user\", origin: \"top-level\" });\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tfor (const root of projectRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\tthis.pathMetadata.set(normalizedPath, { source: \"local\", scope: \"project\", origin: \"top-level\" });\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate isUnderPath(target: string, root: string): boolean {\n\t\tconst normalizedRoot = resolve(root);\n\t\tif (target === normalizedRoot) {\n\t\t\treturn true;\n\t\t}\n\t\tconst prefix = normalizedRoot.endsWith(sep) ? normalizedRoot : `${normalizedRoot}${sep}`;\n\t\treturn target.startsWith(prefix);\n\t}\n\n\tprivate detectExtensionConflicts(extensions: Extension[]): Array<{ path: string; message: string }> {\n\t\tconst conflicts: Array<{ path: string; message: string }> = [];\n\n\t\t// Track which extension registered each tool, command, and flag\n\t\tconst toolOwners = new Map<string, string>();\n\t\tconst commandOwners = new Map<string, string>();\n\t\tconst flagOwners = new Map<string, string>();\n\n\t\tfor (const ext of extensions) {\n\t\t\t// Check tools\n\t\t\tfor (const toolName of ext.tools.keys()) {\n\t\t\t\tconst existingOwner = toolOwners.get(toolName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Tool \"${toolName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\ttoolOwners.set(toolName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check commands\n\t\t\tfor (const commandName of ext.commands.keys()) {\n\t\t\t\tconst existingOwner = commandOwners.get(commandName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Command \"/${commandName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tcommandOwners.set(commandName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check flags\n\t\t\tfor (const flagName of ext.flags.keys()) {\n\t\t\t\tconst existingOwner = flagOwners.get(flagName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Flag \"--${flagName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tflagOwners.set(flagName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn conflicts;\n\t}\n}\n"]}

package/dist/iosm/guide.d.ts

@@ -25,7 +25,28 @@ export interface IosmGuideWriteResult {
     existed: boolean;
     written: boolean;
 }
+type PlaybookFileName = "AGENTS.md" | "IOSM.md";
+export declare function ensureCanonicalPlaybookPath(rootDir: string, canonicalName: PlaybookFileName): {
+    path: string;
+    existed: boolean;
+    renamedFrom?: string;
+};
+export interface AgentsGuideDocumentInput {
+    rootDir: string;
+    cycleId?: string;
+    assessmentSource: "heuristic" | "verified";
+    iosmIndex?: number | null;
+    decisionConfidence?: number | null;
+    goals?: string[];
+    filesAnalyzed?: number;
+    sourceFileCount?: number;
+    testFileCount?: number;
+    docFileCount?: number;
+}
 export declare function buildIosmPriorityChecklist(metrics: IosmMetricRecord<number | null>, limit?: number): IosmPriorityChecklistItem[];
 export declare function buildIosmGuideDocument(input: IosmGuideDocumentInput): string;
+export declare function buildAgentsGuideDocument(input: AgentsGuideDocumentInput, existingContent?: string): string;
 export declare function writeIosmGuideDocument(input: IosmGuideDocumentInput, overwrite: boolean): IosmGuideWriteResult;
+export declare function writeAgentsGuideDocument(input: AgentsGuideDocumentInput, overwrite: boolean): IosmGuideWriteResult;
+export {};
 //# sourceMappingURL=guide.d.ts.map

package/dist/iosm/guide.d.ts.map

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