guide · ai assistants · mcp

Let an AI assistant compare folders, archives and files with Diffoniq

“What changed between these two releases?” “Is the backup on the NAS complete?” “Which lines differ between these two configs?” An AI assistant that has to answer this on its own reads file after file into its context window, and large folders or large files do not fit. With Diffoniq as an MCP server it asks once and gets the result back as structured data — a summary first, then only what differs; folders, ZIP and 7z archives included. One entry in the assistant’s configuration is all it takes.

What the assistant gets

DiffoniqC.exe /mcp speaks the Model Context Protocol (MCP), the way Claude Code, Claude Desktop, Cursor, GitHub Copilot in VS Code and other assistants connect to tools. It offers three tools. All three only read. None of them changes, moves or deletes a file.

Tool	What it answers
`compare_tree`	Two folders or archives: what is different, what exists on one side only, what could not be verified. A folder against a ZIP works too, and archives inside archives are looked into. On request it decides by file content.
`compare_file`	Two text files: the lines that differ, with their line numbers on both sides. Case, spaces and trailing blanks can be ignored.
`sync_preview`	What a synchronization would do: the folders it would create and the files it would copy, rename or, in mirror mode, delete. A plan, not an action.

Every answer starts with a summary of the whole comparison and then lists the entries, kept short enough for the assistant to read in one go. On a large tree it first names the folders with the most differences; the assistant then looks into one of them, asks only for certain states, or pages on. The tools are also available during the trial period.

Why a tool, and not the assistant on its own

Without a comparison tool, an assistant has to build the answer itself: list both trees, read or hash file after file, and reason about what the lists mean. Everything it reads ends up in its context window, and the window is finite. For two configs that works; for two release folders, a backup on a NAS or a pair of large log files it gets slow, expensive or impossible — and the usual shortcuts have gaps of their own.

The task	The assistant on its own	With Diffoniq as its tool
Two large folders	Lists and hashes both trees in many steps; the output of every step goes through its context. A tree with thousands of files does not fit.	One call. The files never enter the assistant’s context; it reads a summary and a bounded list, and zooms into the folders that matter.
Two large files	Reads both files into context, or runs a diff and reads its whole output.	Gets only the lines that differ, with line numbers on both sides. The files can be far larger than the assistant could read.
Is the copy really identical?	Compares names and sizes, or hashes every file itself.	Compares by content with Diffoniq’s hash cache; what it could not verify is reported as unverified, never as identical.
ZIP and 7z archives	Extracts them to a temporary folder first — or skips them.	Opens archives like folders, also nested, also against a plain folder. Nothing is extracted.
Moved or renamed files	Sees one file missing and one file extra.	Sees one pair, and reports whether the content changed as well.
Files a cloud service keeps online only	Reading a OneDrive or Dropbox placeholder downloads it, silently.	Leaves them unread and says how many, unless you allow the download.
“Make them the same”	Writes its own copy or delete commands and runs them.	Can only show the plan. Copying and deleting stay with you.
Same question tomorrow, other machine	Depends on which tools are installed there and how it scripted them.	Same factory settings everywhere; every answer lists the options that were in effect.

In short: the assistant asks the question, Diffoniq does the reading. What the assistant gets back is the result, not the data.

1. Tell the assistant where Diffoniq is

The entries below use the installer’s path. If you use the portable ZIP, put in the folder you unpacked it to.

Claude Code — in a terminal:

claude mcp add diffoniq -- "C:\Program Files\Diffoniq\DiffoniqC.exe" --mcp

Claude Desktop — in claude_desktop_config.json (Settings → Developer → Edit Config):

{
  "mcpServers": {
    "diffoniq": {
      "command": "C:\\Program Files\\Diffoniq\\DiffoniqC.exe",
      "args": ["/mcp"]
    }
  }
}

Cursor — the same mcpServers block in the project’s .cursor\mcp.json, or in %USERPROFILE%\.cursor\mcp.json for all projects.

VS Code with GitHub Copilot — in the project’s .vscode\mcp.json:

{
  "servers": {
    "diffoniq": {
      "type": "stdio",
      "command": "C:\\Program Files\\Diffoniq\\DiffoniqC.exe",
      "args": ["/mcp"]
    }
  }
}

/mcp, -mcp and --mcp mean the same. In Git Bash use --mcp, because that shell rewrites a leading slash into a path.

2. Ask in plain words

Restart the assistant if it asks you to, then ask as you would ask a colleague:

“Compare D:\releases\v1 with D:\releases\v2 and tell me which files changed.”
“Is \\nas\backup\Photos really the same as D:\Photos? Check the contents.”
“What would a mirror of D:\work onto E:\backup\work delete?”
“Which lines differ between app.ini and app.ini.bak in C:\tools\app?”

Most assistants ask you before they use a tool for the first time. Give paths in full (C:\… or \\server\share\…): the server refuses a relative path, because it would depend on the folder the assistant happens to run in.

What it will not do

Change anything. The assistant can see what a synchronization would do, but it cannot run one. Copying, renaming and deleting stay in your hands, in Diffoniq’s window or in your own script.
Download files that a cloud service keeps online only. A placeholder of OneDrive, Dropbox or another provider that uses the Windows cloud files API is left unread and counted as unverified, and the answer says how many. A drive labelled “Google Drive” counts as online only as a whole, because its streaming mode sets no such attributes; a renamed Google Drive is not recognized. The assistant can ask you and then set include_online_only for that one call. To allow it once and for all, add "env": { "DIFFONIQ_MCP_ONLINE": "read" } to the server entry above.
Use your window settings. The tools compare with the factory settings plus what the assistant asks for, so the same question gets the same answer on every machine. Every answer lists the options that were in effect.

Good to know

Each request runs on its own. The server starts Diffoniq for every comparison and ends it again. If you cancel the request in the assistant, the comparison stops; a comparison that runs longer than 15 minutes is stopped as well.
“Not compared” is not “identical”. Without a content check, files of equal size and date are not read. When the answer has to be final, ask the assistant to compare by content; the repeat check uses Diffoniq’s hash cache.
Archives are folders here. A ZIP or 7z file can be either side, also against a plain folder — see Compare two ZIP files.
Noise can be left out. The assistant can exclude patterns such as backup files, apply the .gitignore rules of both trees, and list moved and renamed files on request.
A skill file for Claude Code and Cursor. Download diffoniq-skill.zip and extract it into your .claude\skills\ folder; it contains one folder diffoniq with the skill, which tells the assistant how to use the three tools well: overview first, then zoom in; absolute paths; never report “unverified” as identical.
No MCP? An assistant that can run commands uses the console companion directly: let it write a JSON report with DiffoniqC.exe /report … --out r.json --format json, read the file and act on it.

The full reference, including every parameter, is in the help: Scripting and AI Assistants.

Try it with your own folders

Diffoniq runs on Windows 10 and 11, 64-bit. Every feature is available for 30 days before you decide, the MCP server included.

Try Diffoniq free for 30 days See pricing

Claude, Cursor, Visual Studio Code, GitHub Copilot, OneDrive, Dropbox and Google Drive are trademarks of their respective owners. Diffoniq is not affiliated with any of them.