[BUG] Edit tool strips trailing spaces in Markdown files

I'm running into this issue also and it's a massive problem when you are building documentation systems and having Claude write documentation.

I tried to look into this issue and submit a fix but the offending code is not in this repository.

When you ask for a Markdown document of your coding work in Claud Code, it usually begins with the following type, but when you read the saved .md file, there are no two spaces at the end of the line, so it goes straight to one line.

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**Last Updated**: 2025-11-28
**Version**: v16
**Author**: John Doe

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If I had to make a problematic prompt,
"Please make a short description of Markdown in a Markdown document."

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The issue is still in action.
I'd like to add that I write exact instructions in CLAUDE.md on how to fix the issue (es. after using the Edit tool in md file, check for missing trailing spaces, restore them not using the Edit tool but with sed, ecc...).
Sometimes this works automatically, sometimes I have to remember Claude that.
In both cases, there's a massive usage of wasted tokens just to fix stripped trailing spaces.

Indeed I notice that the Edit tool strips trailing whitespace even if Claude Code tries to use a replacement string containing whitespace.

<details>
<summary>I ran an experiment with Claude to diagnose:</summary>

❯ Let's run an experiment. In src/crystal/tests/util/cli.py try to make the following replacement (with dots representing
spaces):

From:
``
....Returns the command (as a list of strings) to run Crystal on the command line.
....
....When running
``

To:
``
....Returns the command (as a list of strings) to run Crystal on the command line.
....
....Whenever running
``

⏺ Read 1 file (ctrl+o to expand)

⏺ Update(src/crystal/tests/util/cli.py)
⎿ Added 2 lines, removed 2 lines
33 def get_crystal_command() -> list[str]:
34 """
35 Returns the command (as a list of strings) to run Crystal on the command line.
36 -
37 - When running from a frozen macOS app, this returns the path to the Crystal binary.
36 +
37 + Whenever running from a frozen macOS app, this returns the path to the Crystal binary.
38 Otherwise, this returns ['python', '-m', 'crystal'] using the current interpreter.
39 """
40 python = sys.executable

⏺ The edit succeeded. Now let me verify what actually happened to the blank line:

⏺ Bash(git diff HEAD src/crystal/tests/util/cli.py | cat -v)
⎿ diff --git a/src/crystal/tests/util/cli.py b/src/crystal/tests/util/cli.py
index 29df7cec..635b0d3b 100644
--- a/src/crystal/tests/util/cli.py
… +12 lines (ctrl+o to expand)

⏺ The experiment confirms the issue: the Edit tool silently drops trailing spaces from blank lines. The original \n (4
spaces) became \n (empty). The tool accepted the edit without error even though my old_string specified an empty blank line
but the actual file had a 4-space blank line — it matched them as equivalent.

So the behavior is:

• Matching (old_string): blank lines with or without trailing spaces match each other — the tool treats them as equivalent
• Writing (new_string): blank lines are always written as empty (trailing spaces stripped)

This explains why in my earlier work the Edit tool appeared to "work" when reverting the method, but silently corrupted the
blank lines, requiring the Python script fallback to fix them.

</details>

This was fixed in v2.1.88 — Edit and Write no longer strip trailing spaces in .md/.mdx files, preserving Markdown hard line breaks. If you're still seeing this in the latest version, please comment with your version and repro and we'll reopen.

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