moved assistant to use skills; added agent monitoring

apps/cli/src/application/assistant/skills/deletion-guardrails/skill.ts

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+export const skill = String.raw`
+# Deletion Guardrails
+
+Load this skill when a user asks to delete agents or workflows so you follow the required confirmation steps.
+
+## Workflow deletion protocol
+1. Read the workflow file to identify every agent it references.
+2. Report those agents to the user and ask whether they should be deleted too.
+3. Wait for explicit confirmation before deleting anything.
+4. Only remove the workflow and/or agents the user authorizes.
+
+## Agent deletion protocol
+1. Inspect the agent file to discover which workflows reference it.
+2. List those workflows to the user and ask whether they should be updated or deleted.
+3. Pause for confirmation before modifying workflows or removing the agent.
+4. Perform only the deletions the user approves.
+
+## Safety checklist
+- Never delete cascaded resources automatically.
+- Keep a clear audit trail in your responses describing what was removed.
+- If the user’s instructions are ambiguous, ask clarifying questions before taking action.
+`;
+
+export default skill;

apps/cli/src/application/assistant/skills/index.ts

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+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import deletionGuardrailsSkill from "./deletion-guardrails/skill.js";
+import mcpIntegrationSkill from "./mcp-integration/skill.js";
+import workflowAuthoringSkill from "./workflow-authoring/skill.js";
+import workflowRunOpsSkill from "./workflow-run-ops/skill.js";
+
+const CURRENT_FILE = fileURLToPath(import.meta.url);
+const CURRENT_DIR = path.dirname(CURRENT_FILE);
+const CATALOG_PREFIX = "src/application/assistant/skills";
+
+type SkillDefinition = {
+  id: string;
+  title: string;
+  folder: string;
+  summary: string;
+  content: string;
+};
+
+type ResolvedSkill = {
+  id: string;
+  catalogPath: string;
+  content: string;
+};
+
+const definitions: SkillDefinition[] = [
+  {
+    id: "workflow-authoring",
+    title: "Workflow Authoring",
+    folder: "workflow-authoring",
+    summary: "Creating or editing workflows/agents, validating schema rules, and keeping filenames aligned with JSON ids.",
+    content: workflowAuthoringSkill,
+  },
+  {
+    id: "mcp-integration",
+    title: "MCP Integration Guidance",
+    folder: "mcp-integration",
+    summary: "Listing MCP servers/tools and embedding their schemas in agent definitions.",
+    content: mcpIntegrationSkill,
+  },
+  {
+    id: "deletion-guardrails",
+    title: "Deletion Guardrails",
+    folder: "deletion-guardrails",
+    summary: "Following the confirmation process before removing workflows or agents and their dependencies.",
+    content: deletionGuardrailsSkill,
+  },
+  {
+    id: "workflow-run-ops",
+    title: "Workflow Run Operations",
+    folder: "workflow-run-ops",
+    summary: "Commands that list workflow runs, inspect paused executions, or manage cron schedules for workflows.",
+    content: workflowRunOpsSkill,
+  },
+];
+
+const skillEntries = definitions.map((definition) => ({
+  ...definition,
+  catalogPath: `${CATALOG_PREFIX}/${definition.folder}/skill.ts`,
+}));
+
+const catalogSections = skillEntries.map((entry) => [
+  `## ${entry.title}`,
+  `- **Skill file:** \`${entry.catalogPath}\``,
+  `- **Use it for:** ${entry.summary}`,
+].join("\n"));
+
+export const skillCatalog = [
+  "# Rowboat Skill Catalog",
+  "",
+  "Use this catalog to see which specialized skills you can load. Each entry lists the exact skill file plus a short description of when it helps.",
+  "",
+  catalogSections.join("\n\n"),
+].join("\n");
+
+const normalizeIdentifier = (value: string) =>
+  value.trim().replace(/\\/g, "/").replace(/^\.\/+/, "");
+
+const aliasMap = new Map<string, ResolvedSkill>();
+
+const registerAlias = (alias: string, entry: ResolvedSkill) => {
+  const normalized = normalizeIdentifier(alias);
+  if (!normalized) return;
+  aliasMap.set(normalized, entry);
+};
+
+const registerAliasVariants = (alias: string, entry: ResolvedSkill) => {
+  const normalized = normalizeIdentifier(alias);
+  if (!normalized) return;
+
+  const variants = new Set<string>([normalized]);
+
+  if (/\.(ts|js)$/i.test(normalized)) {
+    variants.add(normalized.replace(/\.(ts|js)$/i, ""));
+    variants.add(
+      normalized.endsWith(".ts") ? normalized.replace(/\.ts$/i, ".js") : normalized.replace(/\.js$/i, ".ts"),
+    );
+  } else {
+    variants.add(`${normalized}.ts`);
+    variants.add(`${normalized}.js`);
+  }
+
+  for (const variant of variants) {
+    registerAlias(variant, entry);
+  }
+};
+
+for (const entry of skillEntries) {
+  const absoluteTs = path.join(CURRENT_DIR, entry.folder, "skill.ts");
+  const absoluteJs = path.join(CURRENT_DIR, entry.folder, "skill.js");
+  const resolvedEntry: ResolvedSkill = {
+    id: entry.id,
+    catalogPath: entry.catalogPath,
+    content: entry.content,
+  };
+
+  const baseAliases = [
+    entry.id,
+    entry.folder,
+    `${entry.folder}/skill`,
+    `${entry.folder}/skill.ts`,
+    `${entry.folder}/skill.js`,
+    `skills/${entry.folder}/skill.ts`,
+    `skills/${entry.folder}/skill.js`,
+    `${CATALOG_PREFIX}/${entry.folder}/skill.ts`,
+    `${CATALOG_PREFIX}/${entry.folder}/skill.js`,
+    absoluteTs,
+    absoluteJs,
+  ];
+
+  for (const alias of baseAliases) {
+    registerAliasVariants(alias, resolvedEntry);
+  }
+}
+
+export const availableSkills = skillEntries.map((entry) => entry.id);
+
+export function resolveSkill(identifier: string): ResolvedSkill | null {
+  const normalized = normalizeIdentifier(identifier);
+  if (!normalized) return null;
+
+  return aliasMap.get(normalized) ?? null;
+}

apps/cli/src/application/assistant/skills/mcp-integration/skill.ts

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+export const skill = String.raw`
+# MCP Integration Guidance
+
+Load this skill whenever a user asks about external tools, MCP servers, or how to extend an agent’s capabilities.
+
+## Key concepts
+- MCP servers expose tools (web scraping, APIs, databases, etc.) declared in \`config/mcp.json\`.
+- Agents reference MCP tools through the \`"tools"\` block by specifying \`type\`, \`name\`, \`description\`, \`mcpServerName\`, and a full \`inputSchema\`.
+- Tool schemas can include optional property descriptions; only include \`"required"\` when parameters are mandatory.
+
+## Operator actions
+1. Use \`listMcpServers\` to enumerate configured servers.
+2. Use \`listMcpTools\` for a server to understand the available operations and schemas.
+3. Explain which MCP tools match the user’s needs before editing agent definitions.
+4. When adding a tool to an agent, document what it does and ensure the schema mirrors the MCP definition.
+
+## Example snippets to reference
+- Firecrawl search (required param):
+\`\`\`
+"tools": {
+  "search": {
+    "type": "mcp",
+    "name": "firecrawl_search",
+    "description": "Search the web",
+    "mcpServerName": "firecrawl",
+    "inputSchema": {
+      "type": "object",
+      "properties": {
+        "query": {"type": "string", "description": "Search query"},
+        "limit": {"type": "number", "description": "Number of results"}
+      },
+      "required": ["query"]
+    }
+  }
+}
+\`\`\`
+- ElevenLabs text-to-speech (no required array):
+\`\`\`
+"tools": {
+  "text_to_speech": {
+    "type": "mcp",
+    "name": "text_to_speech",
+    "description": "Generate audio from text",
+    "mcpServerName": "elevenLabs",
+    "inputSchema": {
+      "type": "object",
+      "properties": {
+        "text": {"type": "string"}
+      }
+    }
+  }
+}
+\`\`\`
+
+## Safety reminders
+- Only recommend MCP tools that are actually configured.
+- Clarify any missing details (required parameters, server names) before modifying files.
+`;
+
+export default skill;

apps/cli/src/application/assistant/skills/workflow-authoring/skill.ts

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+export const skill = String.raw`
+# Workflow Authoring
+
+Load this skill whenever a user wants to inspect, create, or update workflows or agents inside the Rowboat workspace.
+
+## Workflow knowledge
+- Workflows (\`workflows/*.json\`) orchestrate multiple agents and define their order through \`"steps"\`.
+- Agents (\`agents/*.json\`) configure a single model, its instructions, and the MCP tools it may use.
+- Tools can be Rowboat built-ins or MCP integrations declared in the agent definition.
+
+## Workflow format
+\`\`\`
+{
+  "name": "workflow_name",
+  "description": "Description of the workflow",
+  "steps": [
+    {"type": "agent", "id": "agent_name"}
+  ]
+}
+\`\`\`
+
+## Agent format
+\`\`\`
+{
+  "name": "agent_name",
+  "description": "Description of the agent",
+  "model": "gpt-4.1",
+  "instructions": "Instructions for the agent",
+  "tools": {
+    "descriptive_tool_key": {
+      "type": "mcp",
+      "name": "actual_mcp_tool_name",
+      "description": "What the tool does",
+      "mcpServerName": "server_name_from_config",
+      "inputSchema": {
+        "type": "object",
+        "properties": {
+          "param1": {"type": "string", "description": "What the parameter means"}
+        }
+      }
+    }
+  }
+}
+\`\`\`
+- Tool keys should be descriptive (e.g., \`"search"\`, \`"fetch"\`, \`"analyze"\`) rather than the MCP tool name.
+- Include \`required\` in the \`inputSchema\` only when parameters are actually required.
+
+## Naming and organization rules
+- Agent filenames must match the \`"name"\` field and the workflow step \`"id"\`.
+- Workflow filenames must match the \`"name"\` field.
+- Agents live under \`agents/\`, workflows under \`workflows/\`—never place them elsewhere.
+- Always keep filenames, \`"name"\`, and referenced ids perfectly aligned.
+- Use relative paths (no \${BASE_DIR} prefixes) when calling tools from the CLI.
+
+## Capabilities checklist
+1. Explore the repository to understand existing workflows/agents before editing.
+2. Update files carefully to maintain schema validity.
+3. Suggest improvements and ask clarifying questions.
+4. List and explore MCP servers/tools when users need new capabilities.
+5. Confirm work done and outline next steps once changes are complete.
+`;
+
+export default skill;

apps/cli/src/application/assistant/skills/workflow-run-ops/skill.ts

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+export const skill = String.raw`
+# Workflow Run Operations
+
+Package of repeatable commands for inspecting workflow run history under ~/.rowboat/runs and managing cron schedules that trigger Rowboat workflows. Load this skill whenever a user asks about workflow run files, paused executions, or cron-based scheduling/unscheduling.
+
+## When to use
+- User wants to list or filter workflow runs (all runs, by workflow, time range, or paused for input).
+- User wants to inspect cron jobs or change the workflow schedule.
+- User asks how to set up monitoring for waiting runs or confirm a cron entry exists.
+
+## Run monitoring examples
+Operate from ~/.rowboat (Rowboat tools already set this as the working directory). Use executeCommand with the sample Bash snippets below, modifying placeholders as needed.
+
+Each run file name starts with a timestamp like '2025-11-12T08-02-41Z'. You can use this to filter for date/time ranges.
+
+Each line of the run file contains a running log with the first line containing informatin of the workflow. E.g. '{"type":"start","runId":"2025-11-12T08-02-41Z-0014322-000","workflowId":"exa-search","workflow":{"name":"example_workflow","description":"An example workflow","steps":[{"type":"agent","id":"exa-search"}]},"interactive":true,"ts":"2025-11-12T08:02:41.168Z"}'
+
+If a run is waiting for human input the last line will contain 'paused_for_human_input'. See examples below.
+
+1. **List all runs**
+   
+   ls ~/.rowboat/runs
+   
+
+2. **Filter by workflow**
+   
+   grep -rl '"workflowId":"<workflow-id>"' ~/.rowboat/runs | xargs -n1 basename | sed 's/\.jsonl$//' | sort -r
+   
+   Replace <workflow-id> with the desired id.
+
+3. **Filter by time window**
+   To the previous commands add the below through unix pipe
+   
+   awk -F'/' '$NF >= "2025-11-12T08-03" && $NF <= "2025-11-12T08-10"'
+   
+   Use the correct timestamps.
+
+4. **Show runs waiting for human input**
+   
+   awk 'FNR==1{if (NR>1) print fn, last; fn=FILENAME} {last=$0} END{print fn, last}' ~/.rowboat/runs/*.jsonl | grep 'pause-for-human-input' | awk '{print $1}'
+   
+   Prints the files whose last line equals 'pause-for-human-input'.
+
+## Cron management examples
+1. **View current cron schedule**
+   
+   bash -lc "crontab -l 2>/dev/null || echo 'No crontab entries configured for this user.'"
+   
+2. **Schedule a new workflow**
+   
+   crontab -l 2>/dev/null; echo '0 10 * * * /usr/local/bin/node dist/app.js exa-search "what is the weather in tokyo" >> /Users/arjun/.rowboat/logs/exa_search.log 2>&1' ) | crontab -
+   
+
+3. **Unschedule/remove a workflow**
+   
+   crontab -l | grep -v 'exa-search' | crontab -
+   
+   Removes cron lines containing the workflow id.
+`;
+
+export default skill;