`clojure_edit` replace reformats entire file via cljfmt, not just the target form causing Noisy diffs and Stale REPL vars

[williamp44]

clojure_edit replace reformats entire file via cljfmt, not just the target form

Summary

When using clojure_edit with operation: "replace" to replace a single top-level form, the pipeline applies cljfmt to the entire file — not just the replaced form. This causes collateral whitespace changes in unrelated code throughout the file causing Noisy diffs and Stale REPL vars

Steps to reproduce

1. Create a Clojure file with intentional alignment spacing:

(ns example.core)

(def ob-yes-heavy
  {:orderbook {:yes [[60 200] [55 150]]
               :no  [[40 80]  [35 60]]}})

(def ob-empty-no  {:orderbook {:yes [[60 100]] :no []}})
(def ob-empty     {:orderbook {:yes [] :no []}})

(defn foo [x] (+ x 1))

(defn bar [x] (+ x 2))

2. Use clojure_edit to replace only the bar function:

file_path: "example.clj"
form_type: "defn"
form_identifier: "bar"
operation: "replace"
content: "(defn bar [x] (+ x 3))"

3. Observe the diff — changes appear outside the replaced form:

 (def ob-yes-heavy
   {:orderbook {:yes [[60 200] [55 150]]
-               :no  [[40 80]  [35 60]]}})
+               :no [[40 80] [35 60]]}})

-(def ob-empty-no  {:orderbook {:yes [[60 100]] :no []}})
-(def ob-empty     {:orderbook {:yes [] :no []}})
+(def ob-empty-no {:orderbook {:yes [[60 100]] :no []}})
+(def ob-empty {:orderbook {:yes [] :no []}})

 (defn foo [x] (+ x 1))

-(defn bar [x] (+ x 2))
+(defn bar [x] (+ x 3))

Only the bar defn should have changed.

Root cause

In pipeline.clj, the edit-form-pipeline function:

1. Locates the target form via find-top-level-form ✅
2. Replaces it with z/replace (scoped to the single form) ✅
3. Converts the zipper back to a string ✅
4. Applies format-source (cljfmt) to the entire file string ← problem

The default cljfmt options in core.clj include aggressive normalizers:

{:remove-surrounding-whitespace? true
 :remove-trailing-whitespace? true
 :remove-consecutive-blank-lines? true
 :insert-missing-whitespace? true
 :remove-multiple-non-indenting-spaces? true}

These rewrite whitespace across the entire file, not just the replaced region.

Impact

For Claude Code / AI agent workflows, this is particularly disruptive:

• Noisy diffs: A single-form replacement produces a diff with dozens of unrelated whitespace changes, making review harder.
• Stale REPL vars: When cljfmt reformats forms surrounding a replaced deftest, Babashka's require :reload doesn't remove old vars that were defined at now-shifted line positions. This causes phantom test failures from ghost test vars that no longer exist in the file but persist in the REPL namespace.

Suggested fix

Any of these would resolve it:

1. Scope cljfmt to only the replaced form — format the new content before inserting it, rather than formatting the whole file after.
2. Make whole-file formatting opt-in — default to formatting only the replaced form; add a config flag like :format-whole-file? true for users who want it.
3. Respect the file's existing style — skip formatting entirely when the operation is replace (the user's provided content is already how they want it).

Workaround: Users can set :cljfmt false in their MCP config to disable the formatting step entirely.

Environment

• clojure-mcp v0.2.6 (commit 35a660b)
• Babashka nREPL
• Claude Code with :cli-assist config profile

[williamp44]

Also, thank you for all the work on clojure-mcp, it works really well and helps immensely! 🙏 << i wholeheartedly agree with this. your project has been a tremendous help with my AI coding projects. if you need any volunteers to help with anything, feel free to let me know.

[bhauman]

Thanks for the detailed write-up! And thanks for the kind words @williamp44 — appreciated.

You've correctly identified the root cause. The formatting step is there primarily as a safety net for paren balancing/repair (parinfer-style), not to enforce style — but the default cljfmt options are more aggressive than they need to be for that purpose.

A couple of options available right now:

1. Disable cljfmt entirely — set :cljfmt false in your config. The paren repair step runs separately before formatting, so you still get delimiter error detection even with cljfmt off.

2. Custom cljfmt config — clojure-mcp picks up directory-based .cljfmt.edn config files. You could use a minimal config that only does indentation without the aggressive whitespace normalizers (e.g., set :remove-multiple-non-indenting-spaces? false).

As for scoping cljfmt to just the affected form — it's feasible in principle. The approach would be to format the replacement content in isolation and re-indent it to match the target position, rather than reformatting the whole file after insertion. There is some complexity here though — since forms aren't necessarily top-level, you need to correctly determine the starting column so the formatted form is properly indented in its new context, which gets tricky. Since it would also be a change in behavior, it'd probably need to be a config option (something like :cljfmt :partial). If that's something you're interested in tackling, PRs are welcome!