AI Assistant
AI Tools Reference Complete list of all 42 tools available to the AI assistant.
The AI assistant has access to 42 specialized tools that it uses automatically based on your requests. You don't need to invoke these manually — just describe what you need in natural language and the AI selects the right tool.
These tools let the AI read, create, and modify files in your project.
Tool What it does listFilesList all files in your workspace with sizes readFileRead file content with line numbers searchInFilesSearch for a pattern across all files (like grep) globFilesFind files matching a pattern (e.g., figures/*.png) editFileFind-and-replace edit in a single file batchEditMultiple find-and-replace edits in one file multiFileEditFind-and-replace across multiple files at once insertAtLineInsert or replace content at a specific line number appendToFileAdd content to the end of a file createFileCreate a new file (.tex, .bib, .cls, .sty, .py, .csv, .json, .yaml) renameFileRename a file in the workspace deleteFilePermanently delete a file updatePaperFileWrite to a paper file (used during initial scaffold setup)
These tools generate formatted LaTeX content.
Tool What it does generateTableGenerate a publication-quality LaTeX table generateEquationGenerate LaTeX equation(s) generatePseudocodeGenerate algorithmicx pseudocode blocks generateDiagramGenerate a Scriptora XML diagram generateFigureLayoutGenerate subfigure/subcaption layouts generateOutlineGenerate a structured paper outline generateSectionGenerate a complete paper section
Tool What it does searchLiteratureSearch OpenAlex, arXiv, PubMed, Semantic Scholar, CrossRef, and CORE fetchAndParsePaperExtract content from a paper PDF URL listReferencePDFsList manually uploaded reference PDFs readReferencePDFRead text from an uploaded PDF searchKnowledgeBaseSemantic search across your uploaded papers and past work getDocumentStatsCount words, sections, citations, figures, and tables analyzeResearchCorpusAnalyze all .tex files as a research corpus
Tool What it does suggestEditPropose an inline tracked diff (you accept or reject) suggestBatchEditPropose multiple inline diffs at once
Tool What it does formatForJournalReformat preamble for a target journal/conference generateCoverLetterWrite a cover letter and save as cover_letter.tex checkSubmissionReadinessRun a submission checklist (title, abstract, citations, etc.) prepareArxivSubmissionSuggest arXiv metadata (category, comments) reviewPaperSimulate a peer review with scores and detailed feedback
Tool What it does compilePaperCompile your LaTeX to PDF executePythonRun Python code in a secure Docker sandbox (60s timeout, no network)
Tool What it does askUserInputAsk you a structured follow-up question with form controls quickChoicePresent multiple-choice options as clickable buttons
These tools are used during the 7-stage creation pipeline :
Tool What it does reportStageProgressAdvance to the next stage in the pipeline requestUserApprovalPause and wait for your confirmation before proceeding presentPapersForSelectionShow found papers for you to select/deselect
You never need to remember tool names. Just describe what you want — "search for papers on attention mechanisms", "generate a bar chart", "fix the compilation errors" — and the AI picks the right tool automatically.