spine-framework 0.4.4 → 0.5.0-rc.5

package/.framework/mcp/tools/cil/project.ts

@@ -1,791 +0,0 @@
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:module_header:module_header" type="module_header" identity="module_header" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Module header for CIL project MCP tools, importing dependencies used for project lifecycle and version management"]
-// CIL[DOC-RESPONSIBILITY responsibility="Import MCP server SDK, Zod, CIL pipeline utilities, and shared database helpers required by this tool module"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-CONTRACT inputs="" outputs="" errors="" side_effects=""]
-// CIL[DOC-MICRO logic_summary="Sets up the module imports and makes the register function available for MCP server wiring" notable_decisions="[]"]
-// CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-STABILITY stability="stable"]
-// CIL[DOC-AUDIENCE audience="ai"]
-
-import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js'
-import { z } from 'zod'
-import { PIPELINE_STATUS_RANK, pipelineRank } from '../../../functions/_shared/cil.js'
-import { adminDb, fetchFunction } from '../../shared/db.js'
-// CIL[DOC-VECTOR type="context" content="purpose='Module header for CIL project MCP tools, importing dependencies used for project lifecycle and version management'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:module_header:module_header"]
-
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:getCompletedSteps:function" type="function" identity="getCompletedSteps" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Compute the list of completed pipeline step indices for a file based on its current status"]
-// CIL[DOC-RESPONSIBILITY responsibility="Convert a file's pipeline status rank into the set of completed step numbers"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts,.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-CONTRACT inputs="file_path: string, fileStatuses: Record<string, string>" outputs="number[]" errors="none" side_effects="none"]
-// CIL[DOC-MICRO logic_summary="Looks up the file status rank, caps it to the maximum rank, and returns a range of completed step numbers" notable_decisions="[]"]
-// CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-STABILITY stability="stable"]
-function getCompletedSteps(file_path: string, fileStatuses: Record<string, string>): number[] {
-  const rank = pipelineRank(fileStatuses[file_path])
-  const maxRank = Math.max(...Object.values(PIPELINE_STATUS_RANK))
-  const capped = Math.min(rank, maxRank)
-  const completed: number[] = []
-  for (let i = 0; i <= capped; i++) completed.push(i)
-  return completed
-}
-// CIL[DOC-VECTOR type="context" content="purpose='Compute the list of completed pipeline step indices for a file based on its current status'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:getCompletedSteps:function"]
-
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:getReadySteps:function" type="function" identity="getReadySteps" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Determine which pipeline steps are ready to be executed next"]
-// CIL[DOC-RESPONSIBILITY responsibility="Return step numbers whose prerequisites are all completed but which are not yet completed"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts,.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-CONTRACT inputs="file_path: string, fileStatuses: Record<string, string>" outputs="number[]" errors="none" side_effects="none"]
-// CIL[DOC-MICRO logic_summary="Iterates steps 0-8 and collects those not completed with all prerequisites fulfilled" notable_decisions="[]"]
-// CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-STABILITY stability="stable"]
-function getReadySteps(file_path: string, fileStatuses: Record<string, string>): number[] {
-  const completed = getCompletedSteps(file_path, fileStatuses)
-  const ready: number[] = []
-  for (let step = 0; step <= 8; step++) {
-    const prerequisites = Array.from({ length: step }, (_, i) => i)
-    if (!completed.includes(step) && prerequisites.every(p => completed.includes(p))) {
-      ready.push(step)
-    }
-  }
-  return ready
-}
-// CIL[DOC-VECTOR type="context" content="purpose='Determine which pipeline steps are ready to be executed next'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:getReadySteps:function"]
-
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:getBlockedSteps:function" type="function" identity="getBlockedSteps" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Identify pipeline steps that are neither completed nor ready to execute"]
-// CIL[DOC-RESPONSIBILITY responsibility="Return step numbers that cannot yet be executed because prerequisites are missing"]
-  // CIL[DOC-STABILITY stability="internal"]
-  // CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts,.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-CONTRACT inputs="file_path: string, fileStatuses: Record<string, string>" outputs="number[]" errors="none" side_effects="none"]
-// CIL[DOC-MICRO logic_summary="Compares all steps 0-8 against completed and ready sets and returns the remainder" notable_decisions="[]"]
-function getBlockedSteps(file_path: string, fileStatuses: Record<string, string>): number[] {
-  const completed = getCompletedSteps(file_path, fileStatuses)
-  const ready = getReadySteps(file_path, fileStatuses)
-  const blocked: number[] = []
-  for (let step = 0; step <= 8; step++) {
-    if (!completed.includes(step) && !ready.includes(step)) blocked.push(step)
-  }
-  return blocked
-}
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:getBlockedSteps:function"]
-
-// CIL[DOC-VECTOR type="context" content="purpose='Identify pipeline steps that are neither completed nor ready to execute'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:calculateProgress:function" type="function" identity="calculateProgress" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Calculate a percentage progress value for a file based on its pipeline status rank"]
-// CIL[DOC-RESPONSIBILITY responsibility="Convert a file's pipeline status rank into a 0-100 progress percentage"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts,.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-CONTRACT inputs="file_path: string, fileStatuses: Record<string, string>" outputs="number" errors="none" side_effects="none"]
-// CIL[DOC-MICRO logic_summary="Divides the capped status rank by the maximum rank and rounds to the nearest integer" notable_decisions="[]"]
-// CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-STABILITY stability="stable"]
-function calculateProgress(file_path: string, fileStatuses: Record<string, string>): number {
-  const rank = pipelineRank(fileStatuses[file_path])
-  const maxRank = Math.max(...Object.values(PIPELINE_STATUS_RANK))
-  return Math.round((Math.min(rank, maxRank) / maxRank) * 100)
-}
-// CIL[DOC-VECTOR type="context" content="purpose='Calculate a percentage progress value for a file based on its pipeline status rank'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:calculateProgress:function"]
-
-// CIL[BEGIN stable_id="~/.framework/mcp/tools/cil/project.ts:register:function" type="function" identity="register" parent="~/.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-MACRO purpose="Register CIL project management and version lifecycle tools on an MCP server"]
-// CIL[DOC-RESPONSIBILITY responsibility="Bind MCP tool handlers for listing projects, reporting status, managing versions, and updating pipeline status"]
-// CIL[DOC-CONTEXT module="mcp/tools/cil/project" layer="mcp" related_files=".framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts,.framework/mcp/tools/cil/project.ts"]
-// CIL[DOC-CONTRACT inputs="server: McpServer" outputs="void" errors="Throws if fetchFunction or database calls fail" side_effects="Registers tools on the provided MCP server and may read or update database records"]
-// CIL[DOC-MICRO logic_summary="Registers a suite of CIL project tools including status reporting, version lifecycle, file selection, and pipeline publishing" notable_decisions="[]"]
-// CIL[DOC-CONFIDENCE pass="second" score="0.90" flags="none"]
-// CIL[DOC-STABILITY stability="stable"]
-export function register(server: McpServer) {
-
-  server.registerTool(
-    'spine_cil_list_projects',
-    {
-      description: 'List all CIL projects registered in the database. Returns project names, repo paths, and basic file/chunk counts.',
-      inputSchema: z.object({}),
-    },
-    async () => {
-      const { data } = await adminDb.from('items').select('id, title, data')
-        .filter('data->>kb_type', 'eq', 'cil_project')
-        .eq('is_active', true)
-        .order('created_at', { ascending: true })
-
-      const projects = (data || []).map((p: any) => ({
-        id: p.id,
-        name: p.title,
-        repo_path: p.data?.repo_path || '',
-        language_mix: p.data?.language_mix || '',
-        file_count: p.data?.file_count || 0,
-        chunk_count: p.data?.chunk_count || 0,
-        ingestion_status: p.data?.ingestion_status || 'not_started',
-        last_ingested_at: p.data?.last_ingested_at || null,
-        selected_paths: p.data?.selected_paths || [],
-      }))
-
-      return { content: [{ type: 'text', text: JSON.stringify({ project_count: projects.length, projects }, null, 2) }] }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_project_status',
-    {
-      description: 'Get the full pipeline status for a CIL project: unique file count (from chunks), chunk count, embedding coverage, documentation coverage, and link counts.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-      }),
-    },
-    async ({ project_id }) => {
-      const PAGE_SIZE = 1000
-
-      const [projectRes, totalChunksRes] = await Promise.allSettled([
-        adminDb.from('items').select('id, title, data').eq('id', project_id).maybeSingle(),
-        adminDb.from('items').select('*', { count: 'exact', head: true })
-          .filter('data->>kb_type', 'eq', 'cil_chunk')
-          .filter('data->>project_id', 'eq', project_id)
-          .eq('is_active', true),
-      ])
-
-      const project = projectRes.status === 'fulfilled' ? projectRes.value.data : null
-      const totalChunks = totalChunksRes.status === 'fulfilled' ? (totalChunksRes.value.count || 0) : 0
-
-      const chunks: any[] = []
-      let from = 0
-      while (true) {
-        const { data, error } = await adminDb.from('items').select('id, data')
-          .filter('data->>kb_type', 'eq', 'cil_chunk')
-          .filter('data->>project_id', 'eq', project_id)
-          .eq('is_active', true)
-          .order('id')
-          .range(from, from + PAGE_SIZE - 1)
-        if (error) break
-        if (!data || data.length === 0) break
-        chunks.push(...data)
-        if (data.length < PAGE_SIZE) break
-        from += PAGE_SIZE
-      }
-
-      const chunkIds = new Set(chunks.map((c: any) => c.id))
-      const embeddedIds = new Set<string>()
-      if (chunkIds.size > 0) {
-        let embFrom = 0
-        while (true) {
-          const { data: embeddings, error: embErr } = await adminDb.from('embeddings').select('document_id')
-            .order('id')
-            .range(embFrom, embFrom + PAGE_SIZE - 1)
-          if (embErr) break
-          if (!embeddings || embeddings.length === 0) break
-          for (const row of embeddings) {
-            if (chunkIds.has(row.document_id)) embeddedIds.add(row.document_id)
-          }
-          if (embeddings.length < PAGE_SIZE) break
-          embFrom += PAGE_SIZE
-        }
-      }
-
-      const embeddedChunks = chunks.filter((c: any) => embeddedIds.has(c.id)).length
-      const documentedChunks = chunks.filter((c: any) => c.data?.macro && c.data?.doc_confidence !== 'unverified_legacy').length
-      const verifiedChunks = chunks.filter((c: any) => c.data?.doc_confidence === 'human_verified').length
-      const aiChunks = chunks.filter((c: any) => c.data?.doc_confidence === 'ai_generated').length
-      const pendingReview = chunks.filter((c: any) => c.data?.review_status === 'pending_review').length
-      const deadCode = chunks.filter((c: any) => c.data?.is_dead_code).length
-
-      const uniqueFilePaths = new Set(chunks.map((c: any) => c.data?.file_path).filter(Boolean))
-
-      return {
-        content: [{
-          type: 'text',
-          text: JSON.stringify({
-            project_id,
-            project_name: project?.title || '',
-            repo_path: project?.data?.repo_path || '',
-            selected_paths: project?.data?.selected_paths || [],
-            pipeline: {
-              files: { total: uniqueFilePaths.size },
-              chunks: {
-                total: totalChunks,
-                dead_code: deadCode,
-                pending_review: pendingReview,
-                embedded: embeddedChunks,
-                embedding_coverage_pct: totalChunks > 0 ? Math.round((embeddedChunks / totalChunks) * 100) : 0,
-                documented: documentedChunks,
-                human_verified: verifiedChunks,
-                ai_generated: aiChunks,
-                doc_coverage_pct: totalChunks > 0 ? Math.round((documentedChunks / totalChunks) * 100) : 0,
-              },
-            },
-          }, null, 2),
-        }],
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_doc_gap_report',
-    {
-      description: 'List chunks that have no AI-generated or human-verified documentation. Use this to find chunks that need to be documented before they can be safely edited.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        limit: z.number().int().min(1).max(100).default(20).optional(),
-      }),
-    },
-    async ({ project_id, limit = 20 }) => {
-      const { data: chunks } = await adminDb.from('items').select('id, title, data')
-        .filter('data->>kb_type', 'eq', 'cil_chunk')
-        .filter('data->>project_id', 'eq', project_id)
-        .filter('data->>doc_confidence', 'eq', 'unverified_legacy')
-        .eq('is_active', true)
-        .limit(limit)
-
-      const undocumented = (chunks || []).map((c: any) => ({
-        chunk_id: c.id,
-        chunk_name: c.data?.chunk_name || '',
-        file_path: c.data?.file_path || '',
-        chunk_type: c.data?.chunk_type || '',
-        line_start: c.data?.line_start || 0,
-        line_end: c.data?.line_end || 0,
-      }))
-
-      const { data: allChunks } = await adminDb.from('items').select('id')
-        .filter('data->>kb_type', 'eq', 'cil_chunk')
-        .filter('data->>project_id', 'eq', project_id)
-        .eq('is_active', true)
-
-      const total = allChunks?.length || 0
-      const undocCount = undocumented.length
-
-      return {
-        content: [{
-          type: 'text',
-          text: JSON.stringify({
-            project_id,
-            summary: {
-              total_chunks: total,
-              undocumented_shown: undocCount,
-              coverage_pct: total > 0 ? Math.round(((total - undocCount) / total) * 100) : 100,
-            },
-            undocumented,
-          }, null, 2),
-        }],
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_get_files_by_status',
-    {
-      description: `Get the ordered work queue for a pipeline step — all files in a project at a given pipeline status.
-Use this at the start of each pipeline step to get the list of files to process.
-Valid statuses: "0-discovered", "1-selected", "2-chunked", "3-documented", "4-chunk-validated", "5-doc-validated", "6-enriched", "7-embedded-mapped", "8-published".
-Returns file_path, chunk_count, and last_updated for each file. Process files in the order returned — complete all steps for one file before moving to the next.`,
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        status: z.string().describe('Pipeline status to filter by, e.g. "0-discovered", "2-chunked"'),
-        include_progress_info: z.boolean().default(false).describe('Include pipeline progress and dependency information'),
-      }),
-    },
-    async ({ project_id, status, include_progress_info }) => {
-      const { data: project } = await adminDb.from('items').select('data')
-        .eq('id', project_id).maybeSingle()
-      if (!project) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: `Project not found: ${project_id}` }) }] }
-      }
-
-      const fileStatuses: Record<string, string> = project.data?.file_statuses || {}
-
-      const matchingPaths = Object.entries(fileStatuses)
-        .filter(([, v]) => v === status)
-        .map(([file_path]) => file_path)
-
-      if (matchingPaths.length === 0) {
-        return {
-          content: [{
-            type: 'text',
-            text: JSON.stringify({ ok: true, project_id, status, file_count: 0, files: [], message: `No files found with status "${status}"` }, null, 2),
-          }],
-        }
-      }
-
-      const { data: chunks } = await adminDb.from('items').select('data')
-        .filter('data->>kb_type', 'eq', 'cil_chunk')
-        .filter('data->>project_id', 'eq', project_id)
-        .eq('is_active', true)
-        .in('data->>file_path' as any, matchingPaths)
-
-      const chunkCountByFile: Record<string, number> = {}
-      for (const c of chunks || []) {
-        const fp = c.data?.file_path
-        if (fp) chunkCountByFile[fp] = (chunkCountByFile[fp] || 0) + 1
-      }
-
-      const files = matchingPaths.map(file_path => {
-        const baseFile = {
-          file_path,
-          status,
-          chunk_count: chunkCountByFile[file_path] || 0,
-        }
-
-        if (include_progress_info) {
-          const completedSteps = getCompletedSteps(file_path, fileStatuses)
-          const readySteps = getReadySteps(file_path, fileStatuses)
-          const blockedSteps = getBlockedSteps(file_path, fileStatuses)
-          
-          return {
-            ...baseFile,
-            completed_steps: completedSteps,
-            ready_for: readySteps,
-            blocked_by: blockedSteps,
-            progress_percentage: calculateProgress(file_path, fileStatuses),
-            can_proceed_to: readySteps
-          }
-        }
-
-        return baseFile
-      })
-
-      return {
-        content: [{
-          type: 'text',
-          text: JSON.stringify({ ok: true, project_id, status, file_count: files.length, files }, null, 2),
-        }],
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_update_pipeline_status_flexible',
-    {
-      description: 'Update pipeline status with dependency tracking and progress monitoring for flexible processing.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        file_path: z.string().describe('File path relative to repo root'),
-        status: z.string().describe('New pipeline status'),
-        step_completed: z.number().optional().describe('Step number that was just completed'),
-        force: z.boolean().default(false).describe('Force update even if dependencies not met'),
-      }),
-    },
-    async ({ project_id, file_path, status, step_completed, force }) => {
-      
-      const { data: project } = await adminDb.from('items').select('data')
-        .eq('id', project_id).maybeSingle()
-      
-      if (!project) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: `Project not found: ${project_id}` }) }] }
-      }
-
-      if (!force) {
-        const fileStatuses = project.data?.file_statuses || {}
-        const completedSteps = getCompletedSteps(file_path, fileStatuses)
-        
-        const statusRequirements: Record<string, number[]> = {
-          '0-discovered': [],
-          '1-selected': [0],
-          '2-chunked': [1],
-          '3-documented': [2],
-          '4-chunk-validated': [3],
-          '5-doc-validated': [4],
-          '6-enriched': [5],
-          '7-embedded-mapped': [6],
-          '8-published': [7],
-        }
-        
-        const requiredSteps = statusRequirements[status] || []
-        const missingSteps = requiredSteps.filter(step => !completedSteps.includes(step))
-        
-        if (missingSteps.length > 0) {
-          return {
-            content: [{
-              type: 'text',
-              text: JSON.stringify({
-                ok: false,
-                error: `Cannot update to ${status}. Missing prerequisite steps: ${missingSteps.join(', ')}`,
-                current_completed: completedSteps,
-                required: requiredSteps
-              })
-            }]
-          }
-        }
-      }
-
-      const fileStatuses = project.data?.file_statuses || {}
-      const previousStatus = fileStatuses[file_path]
-      fileStatuses[file_path] = status
-
-      const { error } = await adminDb.from('items')
-        .update({ 
-          data: { 
-            ...project.data,
-            file_statuses: fileStatuses,
-            last_ingested_at: new Date().toISOString()
-          }
-        })
-        .eq('id', project_id)
-
-      if (error) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: error.message }) }] }
-      }
-
-      const updatedState = {
-        file_path,
-        previous_status: previousStatus,
-        new_status: status,
-        step_completed,
-        completed_steps: getCompletedSteps(file_path, fileStatuses),
-        ready_for: getReadySteps(file_path, fileStatuses),
-        blocked_by: getBlockedSteps(file_path, fileStatuses),
-        progress_percentage: calculateProgress(file_path, fileStatuses)
-      }
-
-      return {
-        content: [{
-          type: 'text',
-          text: JSON.stringify({ ok: true, ...updatedState }, null, 2)
-        }],
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_list_files',
-    {
-      description: 'List indexed files for a CIL project with their status and chunk counts.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        limit: z.number().int().min(1).max(1000).default(100).optional(),
-      }),
-    },
-    async ({ project_id, limit = 100 }) => {
-      const { data: project } = await adminDb.from('items').select('data')
-        .eq('id', project_id).maybeSingle()
-      if (!project) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: `Project not found: ${project_id}` }) }] }
-      }
-
-      const { data: chunks, error } = await adminDb.from('items').select('id, data')
-        .filter('data->>kb_type', 'eq', 'cil_chunk')
-        .filter('data->>project_id', 'eq', project_id)
-        .eq('is_active', true)
-        .limit(limit)
-
-      if (error) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: error.message }) }] }
-      }
-
-      const fileMap: Record<string, { chunk_count: number; statuses: Set<string> }> = {}
-      for (const c of chunks || []) {
-        const fp = c.data?.file_path || ''
-        if (!fp) continue
-        if (!fileMap[fp]) fileMap[fp] = { chunk_count: 0, statuses: new Set() }
-        fileMap[fp].chunk_count += 1
-        if (c.data?.status) fileMap[fp].statuses.add(c.data.status)
-      }
-
-      const fileStatuses: Record<string, string> = project.data?.file_statuses || {}
-      const files = Object.entries(fileMap).map(([file_path, info]) => ({
-        file_path,
-        status: fileStatuses[file_path] || null,
-        chunk_count: info.chunk_count,
-        chunk_statuses: Array.from(info.statuses),
-      })).sort((a, b) => a.file_path.localeCompare(b.file_path))
-
-      return { content: [{ type: 'text', text: JSON.stringify({ ok: true, project_id, file_count: files.length, files }, null, 2) }] }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_list_versions',
-    {
-      description: 'List all versions for a CIL project.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-      }),
-    },
-    async ({ project_id }) => {
-      try {
-        const { data, error } = await adminDb.from('items')
-          .select('id, title, data')
-          .filter('data->>kb_type', 'eq', 'cil_version')
-          .filter('data->>project_id', 'eq', project_id)
-          .order('created_at', { ascending: false })
-        if (error) return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: error.message }) }] }
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, versions: data || [] }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_create_version',
-    {
-      description: 'Create a new CIL version for a project. The version must be valid semver; prerelease versions are automatically marked as iterations.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-        version: z.string().describe('Version string, e.g. "0.1.0" or "0.1.6-dev.467.1"'),
-        base_version: z.string().optional().describe('Optional base version string to copy from'),
-      }),
-    },
-    async ({ project_id, version, base_version }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'create_version', {}, {
-          project_id,
-          version,
-          base_version,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, version: result.version }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_set_active_version',
-    {
-      description: 'Set the active version for a CIL project.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-        version_id: z.string().describe('The cil_version UUID to make active'),
-      }),
-    },
-    async ({ project_id, version_id }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'set_active_version', {}, {
-          project_id,
-          version_id,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, project: result.project, version_id: result.version_id }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_publish_version',
-    {
-      description: 'Publish a new CIL version. Marks all other versions as inactive and sets it as the active and default version.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-        version: z.string().describe('Version string to publish, e.g. "0.2.0"'),
-        base_version: z.string().optional().describe('Optional base version whose prerelease iteration should be linked'),
-      }),
-    },
-    async ({ project_id, version, base_version }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'publish_version', {}, {
-          project_id,
-          version,
-          base_version,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, version: result.version, project: result.project }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_mark_versions_inactive',
-    {
-      description: 'Mark all CIL versions whose version string matches a pattern as inactive.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-        version_pattern: z.string().describe('Substring to match in version strings'),
-      }),
-    },
-    async ({ project_id, version_pattern }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'mark_versions_inactive', {}, {
-          project_id,
-          version_pattern,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, ...result }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_archive_versions',
-    {
-      description: 'Archive the oldest inactive CIL versions, keeping only the most recent N inactive versions.',
-      inputSchema: z.object({
-        project_id: z.string().describe('The cil_project UUID'),
-        keep_last_n: z.number().int().min(0).describe('Number of most recent inactive versions to keep'),
-      }),
-    },
-    async ({ project_id, keep_last_n }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'archive_versions', {}, {
-          project_id,
-          keep_last_n,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, ...result }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_create_project',
-    {
-      description: 'Create a new CIL project for a repository. The project will be created with discovery not yet run.',
-      inputSchema: z.object({
-        title: z.string().describe('Project title'),
-        repo_path: z.string().describe('Absolute path to the repository root'),
-        npm_name: z.string().describe('NPM package name'),
-        canonical_root: z.string().describe('Canonical root prefix for stable IDs'),
-        kind: z.enum(['core', 'custom']).default('custom').describe('Project kind: core (framework) or custom app'),
-        globs: z.array(z.string()).default(['**/*.{ts,tsx,js,jsx}']).optional().describe('Globs for source discovery'),
-        exclude_globs: z.array(z.string()).default(['**/node_modules/**', '**/dist/**', '**/*.d.ts']).optional().describe('Globs to exclude'),
-      }),
-    },
-    async ({ title, repo_path, npm_name, canonical_root, kind, globs, exclude_globs }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'create', {}, {
-          title,
-          repo_path,
-          npm_name,
-          canonical_root,
-          kind,
-          globs,
-          exclude_globs,
-        })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, ...result }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_delete_project',
-    {
-      description: 'Delete a CIL project and all attached records: files, chunks, proposals, versions, suggestions, embeddings, and links.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID to delete'),
-      }),
-    },
-    async ({ project_id }) => {
-      try {
-        const result = await fetchFunction('cil-project', 'delete', { id: project_id })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, ...result }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_select_files',
-    {
-      description: 'Set the selected file paths for a CIL project and advance matching discovered files to 1-selected. Files must already have been discovered (step 0). Only selected files are processed by steps 2-8.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        selected_paths: z.array(z.string()).describe('List of relative file paths or directories to include in ingestion'),
-      }),
-    },
-    async ({ project_id, selected_paths }) => {
-      try {
-        const result = await fetchFunction('cil-ingest', 'select', {}, { project_id, selected_paths })
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: true, ...result }) }] }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-  server.registerTool(
-    'spine_cil_publish',
-    {
-      description: 'Publish a CIL project version and mark all files at 7-embedded-mapped as 8-published. If file_path is provided, only that file is published.',
-      inputSchema: z.object({
-        project_id: z.string().uuid().describe('The cil_project UUID'),
-        version: z.string().describe('Version string to publish, e.g. "0.2.0"'),
-        file_path: z.string().optional().describe('Optional single file to publish'),
-      }),
-    },
-    async ({ project_id, version, file_path }) => {
-      try {
-        const pubResult = await fetchFunction('cil-project', 'publish_version', {}, {
-          project_id,
-          version,
-        })
-
-        const { data: project } = await adminDb.from('items').select('data').eq('id', project_id).maybeSingle()
-        const fileStatuses: Record<string, string> = project?.data?.file_statuses || {}
-        const now = new Date().toISOString()
-        const updated: Record<string, string> = {}
-        for (const [fp, status] of Object.entries(fileStatuses)) {
-          if (file_path && fp !== file_path) continue
-          if (status === '7-embedded-mapped') {
-            updated[fp] = '8-published'
-          }
-        }
-
-        if (Object.keys(updated).length > 0) {
-          const newStatuses = { ...fileStatuses, ...updated }
-          await adminDb.from('items').update({
-            data: { ...project.data, file_statuses: newStatuses, published_at: now },
-            updated_at: now,
-          }).eq('id', project_id)
-        }
-
-        return {
-          content: [{
-            type: 'text',
-            text: JSON.stringify({
-              ok: true,
-              project_id,
-              version,
-              version_id: pubResult.version?.id,
-              published_files: Object.keys(updated).length,
-              file_path: file_path || null,
-            }, null, 2),
-          }],
-        }
-      } catch (err: any) {
-        return { content: [{ type: 'text', text: JSON.stringify({ ok: false, error: err?.message || String(err) }) }] }
-      }
-    }
-  )
-
-}
-// CIL[DOC-VECTOR type="context" content="purpose='Register CIL project management and version lifecycle tools on an MCP server'; No verified external callers; imports: .framework/functions/_shared/cil.ts,.framework/mcp/shared/db.ts"]
-// CIL[DOC-VECTOR type="blast_radius" content="No direct caller data from CIL graph; local impact only"]
-// CIL[DOC-VECTOR type="configuration" content="No environment or build configuration dependencies identified"]
-// CIL[DOC-VECTOR type="constraint" content="Standard runtime; no special invariants documented"]
-// CIL[DOC-VECTOR type="implementation_pattern" content="" status="pending_human_input"]
-// CIL[DOC-VECTOR type="user_journey" content="" status="pending_human_input"]
-// CIL[END stable_id="~/.framework/mcp/tools/cil/project.ts:register:function"]