@seqyuan/annodex 0.1.1 → 0.1.2

package/.next/server/app/page_client-reference-manifest.js

@@ -1 +1 @@
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package/.next/server/app-paths-manifest.json

@@ -18,22 +18,22 @@
   "/api/sessions/route": "app/api/sessions/route.js",
   "/api/soul/route": "app/api/soul/route.js",
   "/favicon.ico/route": "app/favicon.ico/route.js",
-  "/api/agent/[id]/events/route": "app/api/agent/[id]/events/route.js",
+  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
+  "/api/auth/all-providers/route": "app/api/auth/all-providers/route.js",
   "/api/auth/login/[provider]/route": "app/api/auth/login/[provider]/route.js",
   "/api/auth/logout/[provider]/route": "app/api/auth/logout/[provider]/route.js",
-  "/api/auth/all-providers/route": "app/api/auth/all-providers/route.js",
+  "/api/agent/[id]/events/route": "app/api/agent/[id]/events/route.js",
   "/api/auth/providers/route": "app/api/auth/providers/route.js",
-  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
   "/api/internal/runtime/route": "app/api/internal/runtime/route.js",
   "/api/models-config/discover/route": "app/api/models-config/discover/route.js",
-  "/api/models-config/test/route": "app/api/models-config/test/route.js",
   "/api/models-config/route": "app/api/models-config/route.js",
+  "/api/models-config/test/route": "app/api/models-config/test/route.js",
   "/api/models/route": "app/api/models/route.js",
-  "/api/settings/route": "app/api/settings/route.js",
   "/api/reports/[id]/route": "app/api/reports/[id]/route.js",
+  "/api/settings/route": "app/api/settings/route.js",
+  "/api/skills/search/route": "app/api/skills/search/route.js",
   "/api/skills/route": "app/api/skills/route.js",
   "/api/version/route": "app/api/version/route.js",
-  "/api/skills/search/route": "app/api/skills/search/route.js",
   "/api/skills/install/route": "app/api/skills/install/route.js",
   "/login/page": "app/login/page.js",
   "/page": "app/page.js"

package/.next/server/chunks/5582.js

@@ -1,5 +1,5 @@
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package/.next/server/chunks/6429.js

@@ -1,7 +1,7 @@
 "use strict";exports.id=6429,exports.ids=[6429],exports.modules={9805:(a,b,c)=>{c.d(b,{FE:()=>h,zN:()=>i});let d='<widget-capability>\nYou can create interactive visualizations using the `show-widget` code fence.\n\nUse `show-widget` by default when visual output is the primary answer. This includes charts, diagrams, flowcharts, dashboards, UI prototypes, mockups, SVG illustrations, icons, logos, infographics, timelines, hierarchies, comparison views, and visual explanations.\n\nFor diagrams, flowcharts, architecture maps, sequence-style explanations, and Markdown-to-diagram requests, prefer `show-widget` with SVG/HTML over Mermaid. Widgets stream more reliably in this UI. Use Mermaid only when the user explicitly asks for Mermaid source, raw Mermaid, raw Markdown, or a saved Mermaid/Markdown file.\n\nFormat:\n```show-widget\n{"title":"Human-readable title","widget_code":"<raw HTML/SVG string>"}\n```\n\nDetailed specs:\nWhen a `<widget-guidelines>` block is present, follow it. It contains the module-specific design rules for the current request.\n\nRequired rules:\n1. `widget_code` is a JSON string: escape quotes and newlines. Always close the JSON object and fence.\n2. Do not include DOCTYPE, html, head, body, iframe, object, embed, form, link, base, or meta tags.\n3. Keep outer backgrounds transparent. The host supplies theme variables.\n4. Use a single concise widget per fence. For multiple widgets, interleave prose and use a separate `show-widget` fence for each widget.\n5. Streaming order: SVG puts `<defs>` before visible shapes; HTML uses `<style>`, then visible markup, then `<script>` last.\n6. Prefer responsive SVG for static visuals and small HTML widgets for controls.\n7. SVG widgets use `<svg width="100%" viewBox="0 0 680 H">` and keep all content inside the viewBox.\n8. Interactive controls must visibly update the output. For Chart.js, call `chart.update()` after changes.\n9. Clickable drill-down actions call `window.__widgetSendMessage("short request")`.\n10. Cross-widget filters publish with `window.__widgetPublish("topic", { key: "value" })`; other widgets listen for `widget-filter`.\n11. Allowed CDN hosts: `cdnjs.cloudflare.com`, `cdn.jsdelivr.net`, `unpkg.com`, `esm.sh`.\n12. CDN scripts must use an `onload` initializer plus an `if (window.Lib) init();` fallback.\n13. Use `min-height` instead of fixed outer `height` to prevent clipping.\n14. Title should be human-readable in the user\'s language.\n15. Put explanatory prose outside the code fence.\n16. Do not output raw ```svg, ```html, or plain Mermaid for visual answers unless the user explicitly asks for source code, raw Markdown, raw Mermaid, or a saved file.\n17. Do not convert Markdown outlines into Mermaid by default. Render them as a `show-widget` diagram unless Mermaid/source text is explicitly requested.\n</widget-capability>',e=/\n?\s*<widget-capability>[\s\S]*?<\/widget-capability>\s*/g,f=/\n?\s*<visualization_harness>[\s\S]*?<\/visualization_harness>\s*/g,g=/\n?\s*<widget-guidelines\b[^>]*>[\s\S]*?<\/widget-guidelines>\s*/g;function h(a){return a.replace(e,"\n").replace(f,"\n").replace(g,"\n").replace(/\n{3,}/g,"\n\n").trim()}function i(a){return a.includes("<widget-capability>")?a:a.trim()?`${d}
 
 ${a}`:d}},11002:(a,b,c)=>{function d(a){return"agentMessage"===a.type&&"string"==typeof a.text?a.text:"reasoning"===a.type?[...a.summary??[],...a.content??[]].join("\n"):"plan"===a.type&&"string"==typeof a.text?a.text:""}function e(a){return"commandExecution"===a.type?"bash":"fileChange"===a.type?"edit":"mcpToolCall"===a.type?a.tool||a.server||"mcp":"dynamicToolCall"===a.type?a.tool||"tool":a.type}c.d(b,{WK:()=>g,z2:()=>h});class f{constructor(a,b,c,d){this.threadId=a,this.cwd=b,this.connection=c,this.baseInstructions=d,this.listeners=[],this.cleanupFns=[],this._alive=!0,this._isStreaming=!1,this._isCompacting=!1,this._accumulatedText="",this._activeTurnId=null,this._activeAgentItemId=null,this._currentModel=null,this.setupNotifications()}get sessionId(){return this.threadId}get sessionFile(){return""}get isAlive(){return this._alive}get isStreaming(){return this._isStreaming}get isCompacting(){return this._isCompacting}get model(){return this._currentModel}onEvent(a){return this.listeners.push(a),()=>{let b=this.listeners.indexOf(a);-1!==b&&this.listeners.splice(b,1)}}emit(a){for(let b of this.listeners)try{b(a)}catch{}}setupNotifications(){let a=this.connection.onNotification("item/agentMessage/delta",a=>this.handleAgentMessageDelta(a));this.cleanupFns.push(a);let b=this.connection.onNotification("item/completed",a=>this.handleItemCompleted(a));this.cleanupFns.push(b);let c=this.connection.onNotification("turn/completed",a=>this.handleTurnCompleted(a));this.cleanupFns.push(c);let d=this.connection.onNotification("thread/status/changed",a=>this.handleThreadStatusChanged(a));this.cleanupFns.push(d);let e=this.connection.onNotification("thread/compacted",a=>this.handleCompacted(a));this.cleanupFns.push(e);let f=this.connection.onNotification("item/started",a=>this.handleItemStarted(a));this.cleanupFns.push(f)}eventBelongsToThread(a){return a.threadId===this.threadId}handleAgentMessageDelta(a){!this.eventBelongsToThread(a)||this._isStreaming&&(this._activeTurnId=a.turnId,this._activeAgentItemId=a.itemId,this._accumulatedText+=a.delta??"",this.emit({type:"message_update",message:{role:"assistant",content:[{type:"text",text:this._accumulatedText}],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}}))}handleItemStarted(a){if(!this.eventBelongsToThread(a))return;let b=a.item;("commandExecution"===b.type||"fileChange"===b.type||"mcpToolCall"===b.type||"dynamicToolCall"===b.type)&&(this._activeTurnId=a.turnId,this.emit({type:"tool_execution_start",toolCallId:b.id,toolName:e(b)}))}handleItemCompleted(a){if(!this.eventBelongsToThread(a))return;let b=a.item;if(this._activeTurnId=a.turnId,"agentMessage"===b.type){let a=d(b)||this._accumulatedText;this.emit({type:"message_end",message:{role:"assistant",content:[{type:"text",text:a}],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}}),this._accumulatedText="",this._activeAgentItemId=null}else if("reasoning"===b.type){let a=d(b);a&&this.emit({type:"message_update",message:{role:"assistant",content:[{type:"thinking",thinking:a}],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}})}else("commandExecution"===b.type||"fileChange"===b.type||"mcpToolCall"===b.type||"dynamicToolCall"===b.type)&&this.emit({type:"tool_execution_end",toolCallId:b.id,toolName:e(b),result:function(a){if("commandExecution"===a.type){let b=a.aggregatedOutput??"",c=null!==a.exitCode&&void 0!==a.exitCode?`Exit code: ${a.exitCode}`:"";return b?c?`${b}
-${c}`:b:c}return"fileChange"===a.type?JSON.stringify(a.changes??[]):"mcpToolCall"===a.type?a.error?"string"==typeof a.error?a.error:JSON.stringify(a.error):a.result?"string"==typeof a.result?a.result:JSON.stringify(a.result):"":"dynamicToolCall"===a.type?JSON.stringify(a.contentItems??[]):""}(b),isError:"status"in b&&"string"==typeof b.status?"failed"===b.status||"declined"===b.status:"dynamicToolCall"===b.type&&!1===b.success})}handleTurnCompleted(a){this.eventBelongsToThread(a)&&(this._isStreaming=!1,this._activeTurnId=null,this._accumulatedText&&(this.emit({type:"message_end",message:{role:"assistant",content:[{type:"text",text:this._accumulatedText}],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}}),this._accumulatedText=""),this.emit({type:"agent_end",...a.turn?.status==="failed"?{error:a.turn.error?.message??"Turn failed"}:{}}))}handleThreadStatusChanged(a){this.eventBelongsToThread(a)&&a.status?.type==="idle"&&this._isStreaming&&(this._isStreaming=!1,this._activeTurnId=null,this.emit({type:"agent_end"}))}handleCompacted(a){this.eventBelongsToThread(a)&&(this._isCompacting=!1,this.emit({type:"compaction_end"}))}async prompt(a,b){this._isStreaming=!0,this._accumulatedText="",this.emit({type:"agent_start"}),this.emit({type:"message_start",message:{role:"assistant",content:[],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}});try{let c=await this.connection.request("turn/start",{threadId:this.threadId,input:function(a,b){let c=[];for(let d of(a.trim()&&c.push({type:"text",text:a,text_elements:[]}),b??[])){let a=d.mimeType||"image/png";c.push({type:"image",url:`data:${a};base64,${d.data}`})}return c.length>0?c:[{type:"text",text:"",text_elements:[]}]}(a,b),...this.cwd?{cwd:this.cwd}:{},...this._currentModel?.modelId?{model:this._currentModel.modelId}:{},approvalPolicy:"never",sandboxPolicy:{type:"workspaceWrite",writableRoots:[this.cwd],readOnlyAccess:{type:"fullAccess"},networkAccess:!0,excludeTmpdirEnvVar:!1,excludeSlashTmp:!1}});this._activeTurnId=c.turn?.id??null}catch(a){this._isStreaming=!1,this.emit({type:"agent_end",error:a instanceof Error?a.message:String(a)})}}async abort(){if(this._activeTurnId)try{await this.connection.request("turn/interrupt",{threadId:this.threadId,turnId:this._activeTurnId})}catch{}this._isStreaming=!1,this._activeTurnId=null}async setModel(a,b){this._currentModel={provider:a,modelId:b}}async fork(){try{let a=await this.connection.request("thread/fork",{threadId:this.threadId,persistExtendedHistory:!0}),b=a.thread?.id;if(!b)return{cancelled:!0};return{newThreadId:b}}catch{return{cancelled:!0}}}async navigateTree(a){try{let b=await this.connection.request("thread/read",{threadId:this.threadId,includeTurns:!0}),c=b.thread?.turns??[],d=c.findIndex(b=>b.items.some(b=>b.id===a));if(d<0||d>=c.length-1)return{cancelled:!1};let e=c.length-d-1;return await this.connection.request("thread/rollback",{threadId:this.threadId,numTurns:e}),{cancelled:!1}}catch{return{cancelled:!0}}}async compact(){this._isCompacting=!0,this.emit({type:"compaction_start"});try{await this.connection.request("thread/compact/start",{threadId:this.threadId})}catch(a){this._isCompacting=!1,this.emit({type:"compaction_end",errorMessage:a instanceof Error?a.message:String(a)})}}async rename(a){try{await this.connection.request("thread/name/set",{threadId:this.threadId,name:a})}catch{}}destroy(){if(this._alive){for(let a of(this._alive=!1,this._isStreaming=!1,this.cleanupFns))try{a()}catch{}this.cleanupFns=[],this.listeners=[]}}}async function g(a,b){let c=await a.request("thread/start",{cwd:b.cwd,...b.baseInstructions?{baseInstructions:b.baseInstructions}:{},...b.model?{model:b.model.modelId,modelProvider:b.model.provider}:{},approvalPolicy:"never",sandbox:"workspace-write",experimentalRawEvents:!1,persistExtendedHistory:!0}),d=c.thread?.id;if(!d)throw Error("Failed to create codex thread: no thread.id returned");let e=new f(d,b.cwd,a,b.baseInstructions);return b.model?e.setModel(b.model.provider,b.model.modelId):c.model&&e.setModel(c.modelProvider??"codex",c.model),e}async function h(a,b,c){let d=null;try{let c=await a.request("thread/read",{threadId:b,includeTurns:!1});c?.model&&(d={provider:c.modelProvider??c.thread?.modelProvider??"codex",modelId:c.model})}catch{}let e=new f(b,c,a);return d&&e.setModel(d.provider,d.modelId),e}},55132:(a,b,c)=>{c.d(b,{AX:()=>q,Dw:()=>p,HO:()=>n,KR:()=>r,fZ:()=>s,u_:()=>o});var d=c(29021),e=c(33873),f=c(21820),g=c(18477);function h(){return(0,e.join)((0,f.homedir)(),".config","annodex")}function i(){return(0,e.join)(h(),"providers.json")}let j={"gpt-5-codex":{contextWindow:1048576,maxTokens:128e3},"gpt-5.1-codex-max":{contextWindow:1048576,maxTokens:128e3},"gpt-5.1-codex-mini":{contextWindow:1048576,maxTokens:128e3},"gpt-4.1-codex-max":{contextWindow:1048576,maxTokens:32768},"gpt-4.1-codex-mini":{contextWindow:1048576,maxTokens:32768},"deepseek-chat":{contextWindow:1048576,maxTokens:8192},"deepseek-reasoner":{contextWindow:1048576,maxTokens:8192},"deepseek-v3":{contextWindow:1048576,maxTokens:8192},"kimi-k2":{contextWindow:1048576,maxTokens:8192},"moonshot-v1-auto":{contextWindow:1048576,maxTokens:8192},"glm-4-plus":{contextWindow:128e3,maxTokens:4096},"glm-4-flash":{contextWindow:128e3,maxTokens:4096},"qwen-max":{contextWindow:1048576,maxTokens:8192},"qwen-plus":{contextWindow:1048576,maxTokens:8192},"qwen-turbo":{contextWindow:1048576,maxTokens:8192},"qwen3-235b-a22b":{contextWindow:131072,maxTokens:8192}},k=[{id:"gpt-5-codex",name:"GPT-5 Codex",contextWindow:1048576,maxTokens:128e3,input:["text","image"]},{id:"gpt-5.1-codex-max",name:"GPT-5.1 Codex Max",contextWindow:1048576,maxTokens:128e3,input:["text","image"]},{id:"gpt-5.1-codex-mini",name:"GPT-5.1 Codex Mini",contextWindow:1048576,maxTokens:128e3,input:["text","image"]}];function l(){return{providers:[{id:"openai",name:"OpenAI",baseUrl:"https://api.openai.com/v1",apiKey:"",models:[...k]}],defaultProvider:"openai",defaultModel:"gpt-5.1-codex-max"}}function m(){let a=(0,e.join)((0,f.homedir)(),".codex","config.toml");if(!(0,d.existsSync)(a))return null;try{let b=(0,d.readFileSync)(a,"utf-8");return(0,g.qg)(b)}catch{return null}}function n(){let a=i();if(!(0,d.existsSync)(a))return l();try{let b=JSON.parse((0,d.readFileSync)(a,"utf-8"));return{providers:Array.isArray(b.providers)?b.providers.filter(a=>"string"==typeof a.id&&"string"==typeof a.baseUrl):l().providers,defaultProvider:"string"==typeof b.defaultProvider?b.defaultProvider:void 0,defaultModel:"string"==typeof b.defaultModel?b.defaultModel:void 0}}catch{return l()}}function o(a){let b=h();return(0,d.existsSync)(b)||(0,d.mkdirSync)(b,{recursive:!0}),(0,d.writeFileSync)(i(),JSON.stringify(a,null,2),"utf-8"),a}function p(){let a,b=n(),c=(a=m(),a?.model_providers?Object.entries(a.model_providers).filter(([,a])=>"string"==typeof a.base_url).map(([a,b])=>({id:a,name:b.name??a,baseUrl:(b.base_url??"").replace(/\/+$/,""),apiKey:"",models:[]})):[]),d=function(){let a=m();if(!a)return{};let b=a.model_provider,c=a.model_providers?.[b??""]?.name??b;return{model:a.model,providerId:b,providerName:c}}(),e=new Set(b.providers.map(a=>a.id)),f=[...b.providers];for(let a of c)e.has(a.id)||(f.push(a),e.add(a.id));let g=b.defaultModel??d.model??f[0]?.models[0]?.id;return{providers:f,defaultModel:g,defaultProvider:b.defaultProvider??d.providerId,generativeUI:!1!==b.generativeUI,codexDefaults:d}}function q(a,b){let c=b||a.defaultModel;if(!c)return null;let d=function(a,b){for(let c of a.providers)if(c.models.some(a=>a.id===b))return c}(a,c);if(!d&&a.providers.length>0){let b=a.providers[0],c=b.models[0];return c?{provider:b,modelId:c.id}:null}return d?{provider:d,modelId:c}:null}function r(a){let b=[];for(let c of a.providers)for(let a of c.models){let d=j[a.id];b.push({provider:c.id,modelId:a.id,name:a.name||a.id,contextWindow:a.contextWindow??d?.contextWindow,maxTokens:a.maxTokens??d?.maxTokens,input:a.input})}return b}function s(a){let b=q(a,a.defaultModel);if(!b){for(let b of a.providers)if(b.models.length>0)return{provider:b.id,modelId:b.models[0].id};return null}return{provider:b.provider.id,modelId:b.modelId}}},56429:(a,b,c)=>{c.a(a,async(a,d)=>{try{c.d(b,{A4:()=>p,Bj:()=>q,OF:()=>r});var e=c(11002),f=c(46983),g=c(55132),h=c(9805),i=c(71887),j=c(29021),k=c(33873),l=c(21820),m=c(40402),n=a([f,m]);[f,m]=n.then?(await n)():n;class s{constructor(a){this.inner=a,this.listeners=[],this.cleanupEventSub=null,this.idleTimer=null,this.onDestroyCallback=null,this.busyOperations=new Set,this._alive=!0,this._serverConnection=a.connection}get sessionId(){return this.inner.sessionId}get sessionFile(){return this.inner.sessionFile}get cwd(){return this.inner.cwd}isAlive(){return this._alive&&this.inner.isAlive}isBusy(){return this.busyOperations.size>0||this.inner.isStreaming||this.inner.isCompacting}getRuntimeStatus(){return{sessionId:this.sessionId,sessionFile:this.sessionFile,busy:this.isBusy(),operations:[...this.busyOperations],isStreaming:this.inner.isStreaming,isCompacting:this.inner.isCompacting}}start(){this.cleanupEventSub=this.inner.onEvent(a=>{for(let b of(this.resetIdleTimer(),this.listeners))b(a)}),this.resetIdleTimer()}resetIdleTimer(){this.idleTimer&&clearTimeout(this.idleTimer),this.idleTimer=setTimeout(()=>{this.isBusy()?this.resetIdleTimer():this.destroy()},6e5)}onEvent(a){return this.listeners.push(a),()=>{let b=this.listeners.indexOf(a);-1!==b&&this.listeners.splice(b,1)}}onDestroy(a){this.onDestroyCallback=a}async send(a){this.resetIdleTimer();let b=a.type;switch(b){case"prompt":{let b=a.images,c=a.message;return this.trackBusy("prompt",this.inner.prompt(c,b?.map(a=>({data:a.data,mimeType:a.mimeType})))).catch(()=>{}),null}case"abort":return await this.inner.abort(),null;case"get_state":return{sessionId:this.inner.sessionId,sessionFile:"",isStreaming:this.inner.isStreaming,isCompacting:this.inner.isCompacting,autoCompactionEnabled:!0,autoRetryEnabled:!0,model:this.inner.model?{id:this.inner.model.modelId,provider:this.inner.model.provider}:void 0,messageCount:0,pendingMessageCount:0,contextUsage:null,systemPrompt:this.inner.baseInstructions??"",thinkingLevel:"off"};case"set_model":{let{provider:b,modelId:c}=a,d=(0,g.Dw)(),e=(0,g.AX)(d,c);return e?(e.provider.apiKey||e.provider.baseUrl,await this.inner.setModel(e.provider.id,c)):await this.inner.setModel(b,c),{id:c,provider:b}}case"rename":{let b="string"==typeof a.name?a.name:"";return await this.inner.rename(b),null}case"fork":{let a=await this.inner.fork();if("newThreadId"in a)return this.destroy(),{cancelled:!1,newSessionId:a.newThreadId};return{cancelled:!0}}case"navigate_tree":{let b=a.targetId;return{cancelled:(await this.inner.navigateTree(b)).cancelled}}case"compact":return await this.trackBusy("compact",this.inner.compact()),null;case"steer":{let b=a.images,c=a.message;return await this.trackBusy("steer",this.inner.prompt(`[STEER — user intervenes mid-execution]
+${c}`:b:c}return"fileChange"===a.type?JSON.stringify(a.changes??[]):"mcpToolCall"===a.type?a.error?"string"==typeof a.error?a.error:JSON.stringify(a.error):a.result?"string"==typeof a.result?a.result:JSON.stringify(a.result):"":"dynamicToolCall"===a.type?JSON.stringify(a.contentItems??[]):""}(b),isError:"status"in b&&"string"==typeof b.status?"failed"===b.status||"declined"===b.status:"dynamicToolCall"===b.type&&!1===b.success})}handleTurnCompleted(a){this.eventBelongsToThread(a)&&(this._isStreaming=!1,this._activeTurnId=null,this._accumulatedText&&(this.emit({type:"message_end",message:{role:"assistant",content:[{type:"text",text:this._accumulatedText}],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}}),this._accumulatedText=""),this.emit({type:"agent_end",...a.turn?.status==="failed"?{error:a.turn.error?.message??"Turn failed"}:{}}))}handleThreadStatusChanged(a){this.eventBelongsToThread(a)&&a.status?.type==="idle"&&this._isStreaming&&(this._isStreaming=!1,this._activeTurnId=null,this.emit({type:"agent_end"}))}handleCompacted(a){this.eventBelongsToThread(a)&&(this._isCompacting=!1,this.emit({type:"compaction_end"}))}async prompt(a,b){this._isStreaming=!0,this._accumulatedText="",this.emit({type:"agent_start"}),this.emit({type:"message_start",message:{role:"assistant",content:[],model:this._currentModel?.modelId??"",provider:this._currentModel?.provider??"codex"}});try{let c=await this.connection.request("turn/start",{threadId:this.threadId,input:function(a,b){let c=[];for(let d of(a.trim()&&c.push({type:"text",text:a,text_elements:[]}),b??[])){let a=d.mimeType||"image/png";c.push({type:"image",url:`data:${a};base64,${d.data}`})}return 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 annodex has a persistent Analysis Report tab. It is for curated analysis deliverables, not a transcript summary.
 
@@ -10,6 +10,10 @@ When working on scientific or bioinformatics analysis, keep report-worthy conten
 - Do not include ordinary chat, reasoning traces, failed-debug logs, transient guesses, or results superseded by later parameter changes.
 - When an upstream input, threshold, parameter, or method changes, explicitly state which downstream results or interpretations are outdated and need refresh.
 - Prefer evidence-backed statements that cite generated files, tables, figures, scripts, or command outputs.
+- Make the report visually useful when figures exist: include 1-4 representative local image links with Markdown image syntax, for example \`![UMAP colored by cluster](results/umap_clusters.png)\`.
+- For each representative figure, add a one-sentence caption that states what the figure shows and why it matters biologically or analytically.
+- Do not embed every generated image. Curate representative figures by topic, put the rest in the outputs table, and mention counts/directories.
+- Prefer browser-renderable figures in the report preview (PNG/JPG/SVG/HTML). If only PDFs exist, cite the PDF path and, when practical, create or mention a PNG preview.
 - If you ran tools for a bioinformatics/scientific analysis or created result directories, tables, figures, scripts, or reports, you MUST emit an analysis report update before finishing the response.
 - If the analysis produces many PDFs or figure files, do not expand them all in chat. Summarize them in the report by topic, output directory, counts, representative files, and the biological meaning of the figures.
 
@@ -35,6 +39,12 @@ When you have a compact report-worthy update, emit one or more fenced JSON block
 {"topic":"Short current analysis topic","section":"objective|input_data|methods|quality_control|results|interpretation|outputs|reproducibility","action":"append|replace","status":"draft|verified|needs_review|outdated","markdown":"Concise Markdown for the report section.","sources":["results/file.csv","HSPCs/"],"invalidates":["results"],"note":"Short change note."}
 \`\`\`
 
+Markdown quality requirements:
+- Use short paragraphs, compact tables, and local links to evidence files.
+- In \`results\`, lead with the main finding, then show representative figures and captions when available.
+- In \`outputs\`, group files by result type instead of listing a raw directory dump.
+- In \`interpretation\`, distinguish observed result, biological interpretation, and remaining uncertainty.
+
 Only use this fence for durable analysis summaries, not for chat narration or raw logs.
 </analysis-report-guidelines>`,e=/\n?\s*<analysis-report-guidelines>[\s\S]*?<\/analysis-report-guidelines>\s*/g;function f(a){return a.replace(e,"\n").replace(/\n{3,}/g,"\n\n").trim()}function g(a){return a.includes("<analysis-report-guidelines>")?a:a.trim()?`${a.trimEnd()}
 

package/.next/server/functions-config-manifest.json

@@ -10,6 +10,7 @@
         }
       ]
     },
+    "/api/skills": {},
     "/api/skills/install": {}
   }
 }

package/.next/server/middleware-build-manifest.js

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+globalThis.__BUILD_MANIFEST={polyfillFiles:["static/chunks/polyfills-42372ed130431b0a.js"],devFiles:[],lowPriorityFiles:["static/ba8L-XmHpOUZrUOCFVvvj/_buildManifest.js","static/ba8L-XmHpOUZrUOCFVvvj/_ssgManifest.js"],rootMainFiles:["static/chunks/webpack-fcf4a889ecbd753c.js","static/chunks/4bd1b696-e356ca5ba0218e27.js","static/chunks/3794-123fdf632563f469.js","static/chunks/main-app-45a0f19af99d61b6.js"],rootMainFilesTree:{},pages:{"/_app":[]}};

package/.next/server/next-font-manifest.js

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+self.__NEXT_FONT_MANIFEST='{"pages":{},"app":{"/home/runner/work/annodex/annodex/app/layout":["static/media/ec14413c594b3356-s.p.woff2","static/media/7deddc85b7ffd1dc-s.p.woff2"]},"appUsingSizeAdjust":true,"pagesUsingSizeAdjust":false}';

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package/.next/server/pages/404.html

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package/.next/server/server-reference-manifest.json

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