thesis-writer

Thesis Writer

Thesis Writer is a dual-vendor plugin for plan-driven doctoral thesis authoring with Zotero-grounded citations and IEEE-style LaTeX output. One shared source produces complete Claude Code and Codex plugins; vendor mechanics are kept in small, explicit overlays.

What it provides

document-planner ⇄ zotero-research → writer → figure-generator → formatter → reviewer
       │                                                              ⇄ zotero-research
       └─ corpus gap → zotero-source-acquisition → user-approved import ┘

The plugin also includes authorship-session logging and a vendor-specific project initializer. Claude Code initializes CLAUDE.md; Codex initializes AGENTS.md. Both use the same canonical thesis-instruction template.

Prerequisites

• Zotero with a populated research library
• The Deep Zotero MCP server in a Python virtual environment
• Claude Code and/or Codex
• A LaTeX distribution for compilation
• Python 3.10 or newer; matplotlib for figure generation
• For corpus-gap acquisition: installed Google Chrome, a dedicated persistent SSO profile, and a Zotero API key with library write and file access

The local scripts default to C:\local_working_projects\zotero_citation_mcp. Pass --mcp-root on another machine. The generated MCP configuration contains only the resolved virtual-environment interpreter and -m deep_zotero.server; it never copies or prints API keys.

Install or update locally

Build and validate both plugins first:

python scripts\build_plugin.py --vendor all
python scripts\validate_all.py --mcp-root C:\path\to\zotero_citation_mcp

Install or update Codex:

python scripts\install_plugin.py --vendor codex --mcp-root C:\path\to\zotero_citation_mcp --execute

This copies the disposable generated plugin to ~/plugins/thesis-writer, creates the standard personal marketplace entry only when needed, applies Codex's required local cachebuster, and runs codex plugin add thesis-writer@personal. Start a new Codex task after installation so skills and MCP tools are reloaded.

The installer stages and fully configures the replacement before swapping it into place, so a missing MCP interpreter, failed server import, or missing cachebuster cannot destroy a working installation. A custom --marketplace is supported when it follows <root>/.agents/plugins/marketplace.json and --plugin-home is <root>/plugins; the installer reads and uses that marketplace's actual top-level name in the Codex command.

Install or update Claude Code:

python scripts\install_plugin.py --vendor claude --mcp-root C:\path\to\zotero_citation_mcp --execute

The script builds the Claude distribution, updates or registers this repository as the thesis-writer-marketplace, and updates or installs thesis-writer@thesis-writer-marketplace. Restart Claude Code after installation. From the Claude Code interface, published updates can also be applied with /plugin marketplace update thesis-writer-marketplace followed by /plugin update thesis-writer@thesis-writer-marketplace.

Omit --execute to build and show the vendor commands without running them. Codex's plugin files and marketplace entry are still prepared locally so their paths and MCP import can be verified.

Initialize a thesis project

• Claude Code: run /thesis-writer:init.
• Codex: ask to use the thesis-writer-init skill.

If project instructions already exist, the initializer asks before backing up/replacing or merging them. It never silently overwrites an existing backup or produces a reduced fallback template.

Source and build architecture

Repository-root AGENTS.md contains plugin-maintainer instructions, and root CLAUDE.md is a relative symlink to it. These files govern work on this repository; they are not thesis-project templates and are not consumed by the builder. End-user instructions come only from src/templates/thesis-instructions.md.