spine-framework 0.3.124 → 0.3.126

package/.framework/functions/cil-agent-ingest.ts

@@ -0,0 +1,773 @@
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_module_header_1784235266" type="module_header" identity="module_header" parent="none"]
+// CIL[DOC-MACRO purpose="Module header and top-level exports for cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Own module-level imports, exports, and configuration for cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[\".framework/migrations/015_simplify_apps_table.sql\",\"custom/apps/cortex/pages/operations/OperationsDashboard.tsx\",\"custom/apps/portal/pages/ContentPage.tsx\",\".framework/src/components/ui/table-primitives.tsx\",\".framework/src/pages/admin/TypeDetailPage.tsx\",\"\\\"]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="module exports and side effects" errors="none" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Declares module scope, imports dependencies, and exports public surface of cortex.functions.custom_cil-agent-ingest" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-AUDIENCE audience="developer"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: .framework/migrations/015_simplify_apps_table.sql, custom/apps/cortex/pages/operations/OperationsDashboard.tsx, custom/apps/portal/pages/ContentPage.tsx, .framework/src/components/ui/table-primitives.tsx, .framework/src/pages/admin/TypeDetailPage.tsx, \."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+
+
+import { createHandler } from './_shared/middleware'
+import { adminDb } from './_shared/db'
+import { create as adminCreate, update as adminUpdate } from './admin-data'
+import { resolveTypeId } from './_shared/resolve-ids'
+import * as fs from 'fs'
+import * as path from 'path'
+import * as crypto from 'crypto'
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_module_header_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentingestrequest_1784235266" type="interface" identity="agentingestrequest" parent="none"]
+// CIL[DOC-MACRO purpose="Defines the agentingestrequest type contract in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Describe the shape and allowed fields for agentingestrequest"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[\".framework/src/pages/admin/TypeDetailPage.tsx\",\".framework/functions/_shared/principal.ts\",\".framework/src/pages/admin/IntegrationsPage.tsx\",\".framework/migrations/015_simplify_apps_table.sql\",\"custom/apps/cortex/pages/operations/OperationsDashboard.tsx\",\"\\\"]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="type definition for agentingestrequest" errors="none" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Declares TypeScript type/interface agentingestrequest with member definitions" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: .framework/src/pages/admin/TypeDetailPage.tsx, .framework/functions/_shared/principal.ts, .framework/src/pages/admin/IntegrationsPage.tsx, .framework/migrations/015_simplify_apps_table.sql, custom/apps/cortex/pages/operations/OperationsDashboard.tsx, \."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+interface AgentIngestRequest {
+  project_id: string
+  file_id?: string
+  file_path?: string
+  file_hash?: string
+  markers?: AgentParsedMarker[]
+  chunks?: Array<{
+    chunk_id: string
+    documentation: Record<string, any>
+    metadata?: Record<string, any>
+  }>
+  file_ids?: string[]
+  new_file_path?: string
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentingestrequest_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentparsedmarker_1784235266" type="interface" identity="agentparsedmarker" parent="none"]
+// CIL[DOC-MACRO purpose="Defines the agentparsedmarker type contract in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Describe the shape and allowed fields for agentparsedmarker"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[\".framework/src/pages/admin/TypeDetailPage.tsx\",\".framework/functions/_shared/principal.ts\",\".framework/src/pages/admin/IntegrationsPage.tsx\",\".framework/migrations/015_simplify_apps_table.sql\",\"custom/apps/cortex/pages/operations/OperationsDashboard.tsx\",\"\\\"]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="type definition for agentparsedmarker" errors="none" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Declares TypeScript type/interface agentparsedmarker with member definitions" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: .framework/src/pages/admin/TypeDetailPage.tsx, .framework/functions/_shared/principal.ts, .framework/src/pages/admin/IntegrationsPage.tsx, .framework/migrations/015_simplify_apps_table.sql, custom/apps/cortex/pages/operations/OperationsDashboard.tsx, \."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+interface AgentParsedMarker {
+  chunk_id: string
+  start_line: number
+  end_line: number
+  type: string
+  identity: string
+  parent: string
+  attributes?: Record<string, string>
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentparsedmarker_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentparseddocs_1784235266" type="interface" identity="agentparseddocs" parent="none"]
+// CIL[DOC-MACRO purpose="Defines the agentparseddocs type contract in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Describe the shape and allowed fields for agentparseddocs"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[\".framework/src/pages/admin/TypeDetailPage.tsx\",\".framework/functions/_shared/principal.ts\",\".framework/src/pages/admin/IntegrationsPage.tsx\",\".framework/migrations/015_simplify_apps_table.sql\",\"custom/apps/cortex/pages/operations/OperationsDashboard.tsx\",\"\\\"]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="type definition for agentparseddocs" errors="none" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Declares TypeScript type/interface agentparseddocs with member definitions" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: .framework/src/pages/admin/TypeDetailPage.tsx, .framework/functions/_shared/principal.ts, .framework/src/pages/admin/IntegrationsPage.tsx, .framework/migrations/015_simplify_apps_table.sql, custom/apps/cortex/pages/operations/OperationsDashboard.tsx, \."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+interface AgentParsedDocs {
+  macro?: string
+  responsibility?: string
+  context?: Record<string, any>
+  contract?: Record<string, any>
+  micro?: Record<string, any>
+  examples?: Record<string, any>
+  confidence?: { pass: string; score: number; flags: string[] }
+  stability?: string
+  audience?: string
+  raw: Record<string, string>
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_agentparseddocs_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_computefilehash_1784235266" type="function" identity="computefilehash" parent="none"]
+// CIL[DOC-MACRO purpose="Implements computefilehash logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute computefilehash and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[\"custom/apps/cortex/functions/custom_cil-embeddings.ts\",\".framework/functions/_shared/principal.ts\",\".framework/src/pages/admin/TypeDetailPage.tsx\",\".framework/src/pages/admin/IntegrationsPage.tsx\",\".framework/migrations/015_simplify_apps_table.sql\"]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides computefilehash with computeFileHash(content: string inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: custom/apps/cortex/functions/custom_cil-embeddings.ts, .framework/functions/_shared/principal.ts, .framework/src/pages/admin/TypeDetailPage.tsx, .framework/src/pages/admin/IntegrationsPage.tsx, .framework/migrations/015_simplify_apps_table.sql."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function computeFileHash(content: string): string {
+  return crypto.createHash('sha256').update(content, 'utf8').digest('hex')
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_computefilehash_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_estimatetokens_1784235266" type="function" identity="estimatetokens" parent="none"]
+// CIL[DOC-MACRO purpose="Implements estimatetokens logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute estimatetokens and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides estimatetokens with estimateTokens(text: string inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function estimateTokens(text: string): number {
+  return Math.ceil(text.length / 4)
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_estimatetokens_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_normaliseagentchunkcontent_1784235266" type="function" identity="normaliseagentchunkcontent" parent="none"]
+// CIL[DOC-MACRO purpose="Implements normaliseagentchunkcontent logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute normaliseagentchunkcontent and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides normaliseagentchunkcontent with normaliseAgentChunkContent(raw: string inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function normaliseAgentChunkContent(raw: string): string {
+  const lines = raw.replace(/\r\n/g, '\n').split('\n')
+  const filtered = lines.filter(line => {
+    const trimmed = line.trim()
+    return !trimmed.match(/^(?:(?:\/\/|--|#)\s*|<!--\s*)CIL\[(BEGIN|END)/) && !trimmed.match(/^(?:(?:\/\/|--|#)\s*|<!--\s*)CIL\[DOC-/)
+  })
+  const collapsed: string[] = []
+  let lastBlank = false
+  for (const line of filtered) {
+    const isBlank = line.trim() === ''
+    if (isBlank && lastBlank) continue
+    collapsed.push(line)
+    lastBlank = isBlank
+  }
+  return collapsed.join('\n').trim()
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_normaliseagentchunkcontent_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_computeagentchunkhash_1784235266" type="function" identity="computeagentchunkhash" parent="none"]
+// CIL[DOC-MACRO purpose="Implements computeagentchunkhash logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute computeagentchunkhash and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides computeagentchunkhash with computeAgentChunkHash(codeContent: string inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function computeAgentChunkHash(codeContent: string): string {
+  return crypto.createHash('sha256').update(normaliseAgentChunkContent(codeContent)).digest('hex').slice(0, 16)
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_computeagentchunkhash_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentattributes_1784235266" type="function" identity="parseagentattributes" parent="none"]
+// CIL[DOC-MACRO purpose="Implements parseagentattributes logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute parseagentattributes and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides parseagentattributes with parseAgentAttributes(attrString: string inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function parseAgentAttributes(attrString: string): Record<string, string> {
+  const attrs: Record<string, string> = {}
+  const regex = /(\w+)="([^"]*)"/g
+  let match: RegExpExecArray | null
+  while ((match = regex.exec(attrString)) !== null) {
+    attrs[match[1]] = match[2]
+  }
+  return attrs
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentattributes_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentcilmarkers_1784235266" type="function" identity="parseagentcilmarkers" parent="none"]
+// CIL[DOC-MACRO purpose="Implements parseagentcilmarkers logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute parseagentcilmarkers and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides parseagentcilmarkers with parseAgentCilMarkers(lines: string[] inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function parseAgentCilMarkers(lines: string[]): AgentParsedMarker[] {
+  const markers: AgentParsedMarker[] = []
+  const stack: { line: number; attrs: Record<string, string> }[] = []
+
+  for (let i = 0; i < lines.length; i++) {
+    const trimmed = lines[i].trim()
+    const beginMatch = trimmed.match(/^(?:\/\/|--|#)\s*CIL\[BEGIN\s+(.+)\]$/) || trimmed.match(/^<!--\s*CIL\[BEGIN\s+(.+)\]\s*-->$/)
+    const endMatch = trimmed.match(/^(?:\/\/|--|#)\s*CIL\[END\s+chunk_id="([^"]+)"\]$/) || trimmed.match(/^<!--\s*CIL\[END\s+chunk_id="([^"]+)"\]\s*-->$/)
+
+    if (beginMatch) {
+      const attrs = parseAgentAttributes(beginMatch[1])
+      stack.push({ line: i + 1, attrs })
+    } else if (endMatch && stack.length > 0) {
+      const opened = stack.pop()!
+      markers.push({
+        chunk_id: endMatch[1],
+        start_line: opened.line,
+        end_line: i + 1,
+        type: opened.attrs.type || 'unknown',
+        identity: opened.attrs.identity || '',
+        parent: opened.attrs.parent || 'none',
+        attributes: opened.attrs,
+      })
+    }
+  }
+
+  return markers
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentcilmarkers_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentcildocs_1784235266" type="function" identity="parseagentcildocs" parent="none"]
+// CIL[DOC-MACRO purpose="Implements parseagentcildocs logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute parseagentcildocs and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides parseagentcildocs with parseAgentCilDocs(lines: string[], startLine: number, endLine: number inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function parseAgentCilDocs(lines: string[], startLine: number, endLine: number): AgentParsedDocs {
+  const docs: AgentParsedDocs = { raw: {} }
+  for (let i = startLine - 1; i < endLine - 1; i++) {
+    const trimmed = lines[i].trim()
+    const match = trimmed.match(/^(?:\/\/|--|#)\s*CIL\[DOC-(\w+)\s+(.+)\]$/) || trimmed.match(/^<!--\s*CIL\[DOC-(\w+)\s+(.+)\]\s*-->$/)
+    if (!match) continue
+    const key = match[1]
+    const content = match[2]
+    docs.raw[key] = content
+
+    const attrs = parseAgentAttributes(content)
+
+    switch (key) {
+      case 'MACRO':
+        docs.macro = attrs.purpose || content.replace(/^purpose="|"$/g, '')
+        break
+      case 'RESPONSIBILITY':
+        docs.responsibility = attrs.responsibility || content.replace(/^responsibility="|"$/g, '')
+        break
+      case 'CONTEXT':
+        docs.context = attrs
+        break
+      case 'CONTRACT':
+        docs.contract = attrs
+        break
+      case 'MICRO':
+        docs.micro = attrs
+        break
+      case 'EXAMPLES':
+        docs.examples = attrs
+        break
+      case 'EXPORTS':
+        docs.examples = { ...docs.examples, exports: attrs }
+        break
+      case 'CONFIDENCE':
+        docs.confidence = {
+          pass: attrs.pass || 'first',
+          score: parseFloat(attrs.score || '0'),
+          flags: attrs.flags ? attrs.flags.split(',').map((s: string) => s.trim()).filter(Boolean) : [],
+        }
+        break
+      case 'STABILITY':
+        docs.stability = attrs.stability || content.replace(/^stability="|"$/g, '')
+        break
+      case 'AUDIENCE':
+        docs.audience = attrs.audience || content.replace(/^audience="|"$/g, '')
+        break
+    }
+  }
+  return docs
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_parseagentcildocs_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_mapagentdocstochunkdata_1784235266" type="function" identity="mapagentdocstochunkdata" parent="none"]
+// CIL[DOC-MACRO purpose="Implements mapagentdocstochunkdata logic in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Execute mapagentdocstochunkdata and return its computed result"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="return value from function execution" errors="throws on invalid input or runtime failure" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Provides mapagentdocstochunkdata with mapAgentDocsToChunkData(docs: AgentParsedDocs inputs, handling internal flow and returning a result" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+function mapAgentDocsToChunkData(docs: AgentParsedDocs): Record<string, any> {
+  return {
+    macro: docs.macro || docs.raw.MACRO || '',
+    micro: docs.micro?.logic_summary || docs.responsibility || '',
+    description: docs.macro || '',
+    input_spec: docs.contract?.inputs || '',
+    output_spec: docs.contract?.outputs || '',
+    side_effects: docs.contract?.side_effects || '',
+    throws: docs.contract?.errors || '',
+    module: docs.context?.module || '',
+    layer: docs.context?.layer || '',
+    doc_confidence: docs.confidence?.pass === 'second' ? 'ai_generated' : 'from_source',
+    confidence_score: docs.confidence?.score || 0,
+    confidence_flags: docs.confidence?.flags || [],
+    see_also: docs.context?.related_files || '',
+    tags: docs.micro?.notable_decisions || '',
+    depends_on: docs.contract?.dependencies || '',
+    stability: docs.stability || '',
+    audience: docs.audience || '',
+  }
+}
+
+
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_mapagentdocstochunkdata_1784235266"]
+// CIL[BEGIN chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_handler_1784235266" type="variable" identity="handler" parent="none"]
+// CIL[DOC-MACRO purpose="Defines handler configuration or state in cortex.functions.custom_cil-agent-ingest"]
+// CIL[DOC-RESPONSIBILITY responsibility="Hold the value and default configuration for handler"]
+// CIL[DOC-CONTEXT module="cortex.functions.custom_cil-agent-ingest" layer="function" related_files="[]"]
+// CIL[DOC-CONTRACT inputs="none" outputs="value of handler" errors="none" side_effects="none"]
+// CIL[DOC-MICRO logic_summary="Declares handler with initial value or constant binding used by cortex.functions.custom_cil-agent-ingest" notable_decisions="[]"]
+// CIL[DOC-CONFIDENCE pass="second" score="0.95" flags="none"]
+// CIL[DOC-STABILITY stability="stable"]
+// CIL[DOC-VECTOR type="context" content="Layer: function. Direct callers: 0. Direct calls: 0. Related files: none."]
+// CIL[DOC-VECTOR type="blast_radius" content="Direct callers: 0. Total affected: 0."]
+// CIL[DOC-VECTOR type="configuration" content="No configuration dependencies."]
+// CIL[DOC-VECTOR type="constraint" content="No test paths identified."]
+// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
+// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
+export const handler = createHandler(async (ctx, body) => {
+  const action = ctx.query?.action
+  const req = body as AgentIngestRequest
+
+  if (!req?.project_id) throw new Error('project_id is required')
+
+  const { data: projectItem, error: projectError } = await adminDb
+    .from('items')
+    .select('id, title, data')
+    .eq('id', req.project_id)
+    .maybeSingle()
+
+  if (projectError || !projectItem) throw new Error(`Project not found: ${req.project_id}`)
+
+  const repoPath: string = projectItem.data?.repo_path || ''
+
+  
+  if (action === 'get_selected_files') {
+    const selectedPaths = projectItem.data?.selected_paths as string[] | undefined || []
+    const selectedExtensions = req.selected_extensions || (projectItem.data?.selected_extensions as string[] | undefined) || []
+
+    const { data: files } = await adminDb.from('items').select('id, title, data')
+      .filter('data->>kb_type', 'eq', 'cil_file')
+      .filter('data->>project_id', 'eq', req.project_id)
+      .eq('is_active', true)
+
+    const result = (files || []).map((f: any) => {
+      const fd = f.data || {}
+      const filePath = fd.file_path || f.title
+      const absolutePath = repoPath ? path.join(repoPath, filePath.replace(/^\//, '')) : filePath
+      const isSelected = selectedPaths.length === 0 || selectedPaths.some(sp => filePath === sp || filePath.startsWith(sp + '/'))
+      const extMatch = selectedExtensions.length === 0 || (fd.extension && selectedExtensions.includes(fd.extension))
+      let currentHash = null
+      if (isSelected && extMatch && fs.existsSync(absolutePath)) {
+        currentHash = computeFileHash(fs.readFileSync(absolutePath, 'utf-8'))
+      }
+      return {
+        file_id: f.id,
+        file_path: filePath,
+        stored_hash: fd.stored_hash || null,
+        current_hash: currentHash,
+        language: fd.language || 'unknown',
+        status: fd.status || 'not_started',
+        is_selected: isSelected,
+        extension_matches: extMatch,
+      }
+    })
+
+    return {
+      action: 'get_selected_files',
+      project_id: req.project_id,
+      repo_path: repoPath,
+      files: result.filter((f: any) => f.is_selected && f.extension_matches),
+    }
+  }
+
+  
+  if (action === 'store_markers') {
+    const fileId = req.file_id
+    const filePath = req.file_path
+    const fileHash = req.file_hash
+    const markers = req.markers
+
+    if (!fileId) throw new Error('file_id is required')
+    if (!filePath) throw new Error('file_path is required')
+    if (!fileHash) throw new Error('file_hash is required')
+    if (!markers || !Array.isArray(markers)) throw new Error('markers array is required')
+
+    if (!repoPath) throw new Error('Project has no repo_path configured')
+    const absolutePath = path.join(repoPath, filePath.replace(/^\//, ''))
+    if (!fs.existsSync(absolutePath)) throw new Error(`Source file not found on disk: ${absolutePath}`)
+
+    const content = fs.readFileSync(absolutePath, 'utf-8')
+    const computedHash = computeFileHash(content)
+    if (computedHash !== fileHash) throw new Error(`Hash mismatch: provided ${fileHash} != computed ${computedHash}`)
+
+    const lines = content.split('\n')
+    const parsed = parseAgentCilMarkers(lines)
+    const parsedById = new Map(parsed.map(m => [m.chunk_id, m]))
+
+    const providedIds = new Set(markers.map(m => m.chunk_id))
+    const sourceIds = new Set(parsed.map(m => m.chunk_id))
+    const missingInSource = markers.filter(m => !sourceIds.has(m.chunk_id))
+    const extraInSource = parsed.filter(m => !providedIds.has(m.chunk_id))
+    if (missingInSource.length > 0 || extraInSource.length > 0) {
+      throw new Error(
+        `Marker mismatch: missing_in_source=[${missingInSource.map(m => m.chunk_id).join(',')}], extra_in_source=[${extraInSource.map(m => m.chunk_id).join(',')}]`
+      )
+    }
+
+    const chunkTypeId = await resolveTypeId('item', 'cil_chunk')
+
+    const { data: existingChunks } = await adminDb.from('items').select('id, data')
+      .filter('data->>kb_type', 'eq', 'cil_chunk')
+      .filter('data->>file_id', 'eq', fileId)
+      .eq('is_active', true)
+    const existingByChunkId = new Map((existingChunks || []).map((c: any) => [c.data?.chunk_id || c.id, c]))
+
+    const now = new Date().toISOString()
+    const results: any[] = []
+    const errors: string[] = []
+
+    for (const m of markers) {
+      const parsed = parsedById.get(m.chunk_id)!
+      const codeContent = lines.slice(m.start_line, m.end_line - 1).join('\n')
+      const docs = parseAgentCilDocs(lines, m.start_line, m.end_line)
+      const docFields = mapAgentDocsToChunkData(docs)
+      const chunkHash = computeAgentChunkHash(codeContent)
+      const tokenCount = estimateTokens(codeContent)
+
+      const baseData = {
+        kb_type: 'cil_chunk',
+        chunk_id: m.chunk_id,
+        chunk_name: m.identity,
+        file_id: fileId,
+        project_id: req.project_id,
+        file_path: filePath,
+        chunk_type: m.type,
+        parent_id: m.parent === 'none' ? null : m.parent,
+        line_start: m.start_line,
+        line_end: m.end_line,
+        stored_hash: chunkHash,
+        code_content: codeContent,
+        token_count: tokenCount,
+        is_dead_code: false,
+        review_status: 'approved',
+        boundary_confidence: 'high',
+        boundary_source: 'agent_markers',
+        ...docFields,
+      }
+
+      const existing = existingByChunkId.get(m.chunk_id)
+      if (existing) {
+        const newData = { ...existing.data, ...baseData, updated_at: now }
+        const updateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: existing.id } }
+        await adminUpdate(updateCtx, { data: newData, title: `${filePath}::${m.identity}` })
+          .then(() => results.push({ chunk_id: m.chunk_id, action: 'updated', id: existing.id }))
+          .catch((e: any) => errors.push(`${m.chunk_id}: ${e.message}`))
+      } else {
+        await adminCreate(ctx, {
+          entity: 'items',
+          type_slug: 'cil_chunk',
+          title: `${filePath}::${m.identity}`,
+          status: 'active',
+          is_active: true,
+          data: baseData,
+        })
+          .then((newChunk: any) => results.push({ chunk_id: m.chunk_id, action: 'created', id: newChunk.id }))
+          .catch((e: any) => errors.push(`${m.chunk_id}: ${e.message}`))
+      }
+    }
+
+    const { data: fileItem } = await adminDb.from('items').select('id, data').eq('id', fileId).maybeSingle()
+    if (fileItem) {
+      const newFileData = {
+        ...fileItem.data,
+        stored_hash: computedHash,
+        line_count: lines.length,
+        chunk_count: markers.length,
+        has_existing_markers: true,
+        existing_marker_names: markers.map(m => m.identity),
+        ingestion_pass: 2,
+        status: 'pass2_complete',
+        last_status_at: now,
+      }
+      const updateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: fileId } }
+      await adminUpdate(updateCtx, { data: newFileData }).catch((e: any) => errors.push(`file_update: ${e.message}`))
+    }
+
+    return {
+      action: 'store_markers',
+      project_id: req.project_id,
+      file_id: fileId,
+      file_path: filePath,
+      file_hash: computedHash,
+      chunk_count: markers.length,
+      created: results.filter(r => r.action === 'created').length,
+      updated: results.filter(r => r.action === 'updated').length,
+      errors: errors.length > 0 ? errors : undefined,
+      results,
+    }
+  }
+
+  
+  if (action === 'update_documentation') {
+    const chunks = req.chunks
+    if (!chunks || !Array.isArray(chunks)) throw new Error('chunks array is required')
+
+    const now = new Date().toISOString()
+    const results: any[] = []
+
+    for (const c of chunks) {
+      const { data: chunk } = await adminDb.from('items').select('id, data').eq('id', c.chunk_id).maybeSingle()
+      if (!chunk) {
+        results.push({ chunk_id: c.chunk_id, ok: false, error: 'Chunk not found' })
+        continue
+      }
+
+      const newData = { ...chunk.data, ...c.documentation, ...(c.metadata || {}), doc_updated_at: now }
+      const updateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: c.chunk_id } }
+      await adminUpdate(updateCtx, { data: newData })
+        .then(() => results.push({ chunk_id: c.chunk_id, ok: true, error: null }))
+        .catch((e: any) => results.push({ chunk_id: c.chunk_id, ok: false, error: e.message }))
+    }
+
+    return {
+      action: 'update_documentation',
+      project_id: req.project_id,
+      ok: results.every(r => r.ok),
+      updated: results.filter(r => r.ok).length,
+      failed: results.filter(r => !r.ok).length,
+      results,
+    }
+  }
+
+  
+  if (action === 'detect_changes') {
+    if (!repoPath) throw new Error('Project has no repo_path configured')
+
+    let q = adminDb.from('items').select('id, title, data')
+      .filter('data->>kb_type', 'eq', 'cil_file')
+      .filter('data->>project_id', 'eq', req.project_id)
+      .eq('is_active', true)
+    if (req.file_ids && req.file_ids.length > 0) q = (q as any).in('id', req.file_ids)
+
+    const { data: files } = await q
+    const changed: any[] = []
+    const unchanged: any[] = []
+    const missing: any[] = []
+
+    for (const f of files || []) {
+      const fd = f.data || {}
+      const filePath = fd.file_path || f.title
+      const absolutePath = path.join(repoPath, filePath.replace(/^\//, ''))
+      const storedHash = fd.stored_hash || null
+
+      if (!fs.existsSync(absolutePath)) {
+        missing.push({ file_id: f.id, file_path: filePath })
+        continue
+      }
+
+      const content = fs.readFileSync(absolutePath, 'utf-8')
+      const currentHash = computeFileHash(content)
+      if (storedHash && storedHash === currentHash) {
+        unchanged.push({ file_id: f.id, file_path: filePath })
+      } else {
+        changed.push({ file_id: f.id, file_path: filePath, stored_hash: storedHash, current_hash: currentHash })
+      }
+    }
+
+    return {
+      action: 'detect_changes',
+      project_id: req.project_id,
+      changed_count: changed.length,
+      unchanged_count: unchanged.length,
+      missing_count: missing.length,
+      changed,
+      unchanged,
+      missing,
+    }
+  }
+
+  
+  if (action === 'mark_dead') {
+    const fileId = req.file_id
+    if (!fileId) throw new Error('file_id is required')
+
+    const now = new Date().toISOString()
+    const { data: fileItem } = await adminDb.from('items').select('id, title, data').eq('id', fileId).maybeSingle()
+    if (!fileItem) throw new Error(`File not found: ${fileId}`)
+
+    const updateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: fileId } }
+    await adminUpdate(updateCtx, {
+      is_active: false,
+      data: { ...fileItem.data, is_dead_code: true },
+    })
+
+    const { data: chunks } = await adminDb.from('items').select('id')
+      .filter('data->>kb_type', 'eq', 'cil_chunk')
+      .filter('data->>file_id', 'eq', fileId)
+
+    for (const c of chunks || []) {
+      const chunkUpdateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: c.id } }
+      await adminUpdate(chunkUpdateCtx, { is_active: false }).catch(() => { /* non-fatal */ })
+    }
+
+    return {
+      action: 'mark_dead',
+      project_id: req.project_id,
+      file_id: fileId,
+      file_path: fileItem.data?.file_path || fileItem.title || '',
+      chunks_marked_dead: chunks?.length || 0,
+    }
+  }
+
+  
+  if (action === 'update_file_path') {
+    const fileId = req.file_id
+    const newFilePath = req.new_file_path
+    if (!fileId) throw new Error('file_id is required')
+    if (!newFilePath) throw new Error('new_file_path is required')
+
+    const now = new Date().toISOString()
+    const { data: fileItem } = await adminDb.from('items').select('id, title, data').eq('id', fileId).maybeSingle()
+    if (!fileItem) throw new Error(`File not found: ${fileId}`)
+
+    const oldPath = fileItem.data?.file_path || fileItem.title || ''
+    const newData = { ...fileItem.data, file_path: newFilePath }
+
+    const updateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: fileId } }
+    await adminUpdate(updateCtx, { title: newFilePath, data: newData })
+
+    const { data: chunks } = await adminDb.from('items').select('id, data')
+      .filter('data->>kb_type', 'eq', 'cil_chunk')
+      .filter('data->>file_id', 'eq', fileId)
+
+    for (const c of chunks || []) {
+      const cd = c.data || {}
+      const chunkUpdateCtx = { ...ctx, query: { ...ctx.query, entity: 'items', id: c.id } }
+      await adminUpdate(chunkUpdateCtx, {
+        data: { ...cd, file_path: newFilePath },
+      }).catch(() => { /* non-fatal */ })
+    }
+
+    return {
+      action: 'update_file_path',
+      project_id: req.project_id,
+      file_id: fileId,
+      old_path: oldPath,
+      new_path: newFilePath,
+      chunks_updated: chunks?.length || 0,
+    }
+  }
+
+  throw new Error(`Unknown action: ${action}. Valid actions: get_selected_files, store_markers, update_documentation, detect_changes, mark_dead, update_file_path`)
+})
+
+
+
+// CIL[END chunk_id="custom_apps_cortex_functions_custom_cil_agent_ingest_handler_1784235266"]