Safe multi-patch editing in a single session — avoid the partial-read self-revert trap. Use when editing a file with multiple sequential `patch` tool calls, when a patch warning says 'file was last read with offset/limit pagination', when reviewing your own diff before commit, or when `git diff` shows fewer changes than you intended (the patch silently reverted earlier inserts). Anti-pattern: firing 3+ `patch` calls on a file you first read with `read_file(..., offset=N, limit=M)` and assuming the tool tracks the full file state across calls.
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name
patch-tool-safe-editing
version
1.5.0
description
Safe multi-patch editing in a single session — avoid the partial-read self-revert trap. Use when editing a file with multiple sequential `patch` tool calls, when a patch warning says 'file was last read with offset/limit pagination', when reviewing your own diff before commit, or when `git diff` shows fewer changes than you intended (the patch silently reverted earlier inserts). Anti-pattern: firing 3+ `patch` calls on a file you first read with `read_file(..., offset=N, limit=M)` and assuming the tool tracks the full file state across calls.
changelog
["1.1.0 (2026-07-12): Added '3-retry loop on a stale read' pitfall — when the runtime returns `same_tool_failure_warning; count=3`, do NOT try a 4th patch variation. Stop, re-read full file, or switch to `write_file` / `execute_code` text replacement. Verified on merge_train #42 / PR #41 follow-up.","1.2.0 (2026-07-20): Added 'Mock attribute reassignment is read-once' pitfall — the same 'your mental model of the object is stale' trap as the file-read case, applied to Python `unittest.mock`. Verified on $GITHUB_REPOSITORY PR #8475 (multi-verse opt-in fix, issue #8474) when extending the `create_campaign_upgrade_game_state` helper with opt-in flag support.","1.3.0 (2026-07-20): Added 'string-presence assertion can't catch semantic breakage' pitfall — tests asserting `assert '<broken literal>' in source_text` will pass whether the literal is broken or fixed; the right invariant is subprocess exit code or structural parse, not substring match. Verified against `test_bug_hunt_uses_one_shot_hermes_not_fire_and_forget_ao` which was locking in the broken `hermes agent` CLI form.","1.4.0 (2026-07-20): Added 'indented-block-string `patch` re-indentation collapse' pitfall — when `old_string` contains shared leading-indent whitespace that's identical between lines inside and outside the matched block, the fuzzy matcher replaces only the inner substring and the OUTER surrounding lines shift by the indent delta, producing an unreadable mixed-indent collapse. Fix: rewrite the file with `write_file` instead of chained `patch` calls when the block spans N+ levels of indentation.","1.5.0 (2026-08-01): Added 'patch reports success but disk content is unchanged' pitfall — `patch` returned a `files_modified` ack and a clean unified diff in the response, but the file on disk was byte-identical before and after (verified via `wc -c` + grep for a unique line that should have appeared post-patch). `git diff HEAD` showed nothing (working tree clean — proves the patch didn't land, doesn't prove it was applied as claimed). Same-class trigger: any `patch` call where the target file lives in a freshly-created git worktree (`git worktree add ... origin/main`) AND the file was loaded into the harness via a `terminal(grep ...)` pattern (not via `read_file`). The harness may resolve the path relative to the main worktree, not the new worktree. Verified 2026-08-01, [PR #38](https://github.com/jleechanorg/user_scope/pull/38) — two `patch` calls (one script, one test) both returned success but left the files unchanged; a live `python3 scripts/cmux_resume_watchdog.py --scan-only` then ran the OLD code via Python bytecode cache, masking the failure for a full smoke-test cycle. Fix: rewrite the file via `write_file` (overwrite works regardless of harness path resolution) OR via `execute_code(text.replace(...) + open(...).replace(tmp))` with an atomic `os.replace`. Stronger tripwire than Rule 3's `git diff` tripwire: after every `patch` call on a freshly-created worktree, run `wc -c <file>` and `grep -c '<unique new line>' <file>` BEFORE the live smoke test, and re-read the file with `read_file` to confirm the new line is on disk."]
patch-tool safe editing — avoid the self-revert trap
The trap
The patch tool uses fuzzy matching across the file's CURRENT text, not against what you read. If you read a file with read_file(path, offset=1, limit=100) to confirm a section before patching, then make 3 sequential patches, the file's current text on disk has CHANGED between calls. The tool tracks the disk version, not your mental model.
The actual failure mode (verified 2026-07-09, dark-factory /af wiring):
patch(old_string="# Factory bead ... # this is the 1-line PROMPT comment\n\n# Optional Slack...", new_string="# Pull bead body... 40-line block again... PROMPT=...") → ❌ TOOL REVERTS step 2 because old_string matches lines 1-120 of the post-step-2 disk version which contains the new 40-line block, so the tool's fuzzy match latches onto that block as part of "old_string" and removes it. You have just un-done step 2.
Result:git diff shows your step-3 fix but NOT step-2's 40-line insert. You commit. PR has the bug fix but missing the goal wiring.
The warning you missed
After step 3 above, the patch tool returned:
{"_warning":"/path/to/factory-ao-remediate.sh was last read with offset/limit pagination (partial view). Re-read the whole file before overwriting it."}
This warning means: "your mental model of the file is stale, the next patch may operate against text you don't know exists." It is a soft guardrail, not a hard failure — the patch still ran, but if you keep firing patches without re-reading, the next one is at high risk of partial-match corruption.
The rules
Rule 1 — Re-read the full file before any patch after a partial read
If you read a file with read_file(path, offset=N, limit=M) and N > 1 || M < total_lines, your mental model is partial. ( — the max is 2000).
Before the next patch on that file, re-read it without pagination
read_file(path, offset=1, limit=2000)
# CORRECT — full re-read between patches
read_file("foo.sh", offset=1, limit=500) # initial scan
patch(...)
read_file("foo.sh", offset=1, limit=2000) # mandatory before next patch
patch(...)
read_file("foo.sh", offset=1, limit=2000) # again, if next patch is large
patch(...)
Rule 2 — One patch per file in a turn (when possible)
If you have multiple edits to the same file, do them as a single write_file (full rewrite) instead of multiple patch calls. The write_file is unambiguous — you write the entire final file content. The only downside is having to read the full file first.
For files ≤ ~200 lines, write_file after a single read_file is almost always faster than multiple patch calls.
For files > 200 lines, prefer patch with fresh full-read between every call if a write_file rewrite would risk introducing unrelated changes.
Rule 3 — git diff is your tripwire
After every patch sequence on a file, run git diff --stat -- <file> and read the line counts against your expectation. If the diff shows 2 files changed with +10 / -1 and you intended +50, you have a self-revert.
# After a patch sequence:cd <worktree>
git diff --stat -- daemon/factory-ao-remediate.sh
# daemon/factory-ao-remediate.sh | 10 +++- 1 - ← expected +43 if you added a 43-line block + 1 line comment# daemon/factory-ao-remediate.sh | 10 +++- 1 - ← 10 lines instead of 43: SELF-REVERT
Rule 4 — Never patch a "placeholder comment" you intend to expand
This is the specific anti-pattern that caused the dark-factory self-revert:
# Step 1 — insert a placeholder comment where the big block will go
patch(old_string="PROMPT=\"...\"",
new_string="# Factory bead ${BEAD_ID}: ...\n# TODO: prepend /goal") # ← placeholder# Step 2 — later, "expand" the placeholder
patch(old_string="# Factory bead ${BEAD_ID}: ...\n# TODO: prepend /goal",
new_string="# 40-line block with /goal prefix and br show --json body\nPROMPT=\"/goal\n...") # ← expansion
The old_string in step 2 is ambiguous because the 1-line placeholder appears MULTIPLE TIMES across the file (each bead prompt template, each factory invocation). The tool picks one and your step-1 insert is at risk. The fix: do step 1 + step 2 in a single patch, or re-read the full file before step 2.
Rule 5 — Prefer unique context anchors
When constructing old_string, include 3-5 lines of UNIQUE surrounding context (function name above, variable assignment below, specific comment) so the fuzzy matcher has exactly one place to latch onto. Avoid bare PROMPT=... — too generic.
git diff <file> | head -50 — see if a previous patch's insert is now MISSING
Check the tool's _warning field from each prior patch call — partial-read warnings point to the cause
Fix: re-read the full file, then re-apply the missing patch. Verify with another git diff.
Anti-patterns
❌ Firing 3+ patches on a file after a single partial-read without intermediate re-reads
❌ Patching "placeholder comments" you intend to expand later
❌ Trusting the tool's success message without git diff verification
❌ Using bare PROMPT=, echo, or other generic lines as old_string anchors
❌ Mixing write_file and patch on the same file in one turn
Pitfall — the 3-retry loop on a stale read (added 2026-07-12)
When patch returns a _warning saying the file was last read with offset/limit pagination, the runtime issues a hard backoff signal: after 3 same-file patch attempts (whether variations on old_string or different regions), the tool returns same_tool_failure_warning; count=3; patch has failed 3 times this turn. This looks like a loop. and refuses to keep guessing.
The trap: the natural response to a failed patch is "let me try again with a slightly different anchor" — but every subsequent patch on a stale-read file hits the same fuzzy-match risk. The third attempt is the runtime's hard stop, NOT a license to keep trying. Verified case 2026-07-12 (merge_train #42 / PR #41 follow-up): I read tests/test_conflict_helper.py with read_file(..., offset=1, limit=170), then fired three patch calls anchored on the docstring region. The third failed with the 3-strikes warning; the fix was a single execute_code block that did open().read().replace(old, new, 1) then open().write() to bypass the stale-read anchor entirely.
The recipe when you see the 3-strikes warning:
Stop patching immediately. Do not try a 4th variation.
Re-read the file in full (read_file(path, offset=1, limit=2000)) before any further edit on that file.
If the next edit is large or spans multiple regions, switch to write_file — full file rewrite, no fuzzy-match risk.
For complex multi-region edits, use execute_code with Python text replacement (text.replace(old, new, 1)). This is the most reliable path when patch keeps anchoring on the wrong region.
Verify with git diff --stat -- <file> after the change to confirm the line counts match your intent.
The same pattern applies to ANY tool with a same-tool-failure counter (e.g. execute_code syntax errors, mcp__slack__* repeated calls with the same args). When the runtime warns you that you're looping, the next move is to change the approach, not the inputs.
When to use write_file instead of patch
Scenario
patch
write_file
File ≤ ~200 lines, small change
❌ overkill
✅ single call, no risk
File > 200 lines, single edit
✅ targeted
❌ rewrite is risky
File > 200 lines, multiple edits to same region
✅ re-read between
❌
File > 200 lines, multiple edits to different regions
✅ one patch per region + re-reads
❌
New file
n/a
✅ always
You read the file with offset=N or limit=M last
❌ must re-read full first
✅ write_file forces a clean reset
Reference session
Verified 2026-07-09, dark-factory /af wiring PR jleechanorg/dark-factory#218: the /goal builtin block (40 lines + PROMPT rewrite) in daemon/factory-ao-remediate.sh was reverted by a subsequent patch that anchored on the 1-line placeholder comment. Detected via git diff --stat showing +10 instead of expected +43. Re-applied the missing block via a fresh patch anchored on the full post-step-2 file content (after full re-read), verified with git diff --stat returning the expected line count, then committed + pushed + opened PR.
Pitfall — Mock() attribute reassignment is read-once (added 2026-07-20)
The same "your mental model of the object is stale" trap that bites file edits also bites Python unittest.mock attribute assignment. The hard rule is counter-intuitive: setting a Mock attribute has NO effect on previously-read references to that attribute on the same Mock.
from unittest.mock import Mock
mock = Mock()
# Step 1: read the attribute — Python looks up the attribute descriptor on Mock,# finds nothing, and creates an auto-Mock. The Python-level reference `custom_state`# is now bound to that auto-Mock object, NOT a property descriptor on `mock`.
custom_state = mock.custom_campaign_state
# type(custom_state) -> <class 'unittest.mock.Mock'> ← an auto-generated Mock# Step 2: assign a real dict to the same attribute on `mock`.
mock.custom_campaign_state = {"real": "dict"}
# Step 3: mutate via the earlier reference — looks like it should work, but...
custom_state["real"] = "updated"# TypeError: 'Mock' object does not support item assignment
The fix: bind mock_state.custom_campaign_state to the local variable ONLY AFTER you have assigned it. Do not pre-read it.
mock_state = Mock()
# Order matters: ASSIGN FIRST, then alias to a local
mock_state.custom_campaign_state = {"real": "dict"}
custom_state = mock_state.custom_campaign_state # ← now this is the real dict
custom_state["real"] = "updated"# ✅ works
Verified case 2026-07-20, $GITHUB_REPOSITORY PR #8475 (issue #8474, multi-verse opt-in fix): extending the create_campaign_upgrade_game_state test helper with opt-in flag support. First attempt read mock_state.custom_campaign_state into a local BEFORE the dict assignment in the same function — the local captured the auto-Mock, and the subsequent custom_state["divine_upgrade_available"] = True raised TypeError: 'Mock' object does not support item assignment. Diagnostic recipe: if you see this error in a test helper, the fix is almost always "rebind the local after the assignment" — not "the dict is wrong".
Cross-reference: this is the Python-test equivalent of the file-read pitfall (Rule 1). The trap is the same — your mental model of the object is stale.
When a test asserts assert "<literal broken string>" in source_text, the test PASSES forever as long as that literal substring is anywhere in the source file — even when the substring represents a broken CLI invocation / config key / API call. Verified 2026-07-20: test_bug_hunt_uses_one_shot_hermes_not_fire_and_forget_ao was passing on origin/main because it asserted assert "hermes agent --agent" in text. The actual hermes agent --agent X ... invocation in scripts/bug-hunt-daily.sh was failing at runtime (hermes: error: argument command: invalid choice: 'agent') — but the test couldn't catch it because it was just checking for the presence of the literal broken pattern.
This is structurally similar to the file-read pitfall: the test was asking "does the broken pattern appear?" when it should have been asking "does the working pattern execute?" The first question is satisfiable by the broken code; the second is not.
Fix recipes for the three flavors of string-presence assertion:
# Flavor 1: shell-script invocation# WRONG
text = open("scripts/foo.sh").read()
assert"hermes agent --agent"in text # passes whether or not the command works# RIGHT (option A) — execute and check exit codeimport subprocess
result = subprocess.run(["bash", "-n", "scripts/foo.sh"], capture_output=True)
assert result.returncode == 0# For real invocation: subprocess.run(["bash", "-c", open("scripts/foo.sh").read()],# capture_output=True, timeout=5, env=stub_env)# RIGHT (option B) — structural parse of the assertion targetimport re
m = re.search(r"hermes\s+(-z|--agent)\s", text)
assert m and m.group(1) == "-z", f"expected hermes one-shot, got {m.group(1) if m else'none'}"
# Flavor 2: config key presence# WRONG
text = open("config.yaml").read()
assert"rate_limit_per_minute: 25"in text # passes when the config is corrupted upstream# RIGHTimport yaml
cfg = yaml.safe_load(text)
assert cfg["rate_limit_per_minute"] == 25and0 < cfg["rate_limit_per_minute"] <= 10000
# Flavor 3: regex-match against code that should NOT contain a forbidden pattern# This one is OK — the existence of the forbidden literal IS the bug.# But the test will pass on git-restore even when the source is broken, so pair with# a positive control: assert the working pattern IS present too.assert"hermes -z"in text
assert"hermes agent --agent"notin text # forbidden literal
The principle: any test that asserts "the broken pattern is present" without verifying "the broken pattern WORKS" or "the working pattern executes" cannot catch a broken-string regression. When patching broken code, grep for tests asserting the broken literal and update them in the SAME commit — otherwise the test will keep passing on broken code indefinitely.
Cross-reference: this is the testing-side counterpart to the file-read pitfall (Rule 1) and the Mock attribute pitfall (above). The trap is the same — the test is checking for the wrong kind of invariant.
Pitfall — patchold_string re-indentation collapse on indented blocks (added 2026-07-20)
A subtle failure mode in patch's fuzzy matcher: when old_string and new_string differ only in indentation depth of an inner block (e.g. the new_string has all lines dedented by 4 spaces because they left an enclosing else:), the fuzzy matcher succeeds but the surrounding context loses track of the block's indentation. The replaced region ends up with mixed indentation (lines correctly indented, then off-by-4 lines, then back to the expected depth) and the file becomes unreadable.
Reproducer pattern:
# Phase 1 — patch moves a block out of an `else:`# old_string (mixed-indent common lines):"""Every intent in routing-eval.jsonl must match a trigger in the RESOLVER entry.
Match rule: ...
"""import re
text = RESOLVER.read_text()
...
# new_string (12 spaces, as if it left else:, but it's at class body level → WRONG):"""Every intent in routing-eval.jsonl must match a trigger in the RESOLVER entry.
Match rule: ...
"""import re
text = RESOLVER.read_text()
...
The fuzzy matcher sees 8 spaces → 12 spaces everywhere and replaces naively. Result: the function body's import re etc. are dedented back OUT of the method body. The next test run produces IndentationError: unexpected indent or unindent does not match any outer indentation level on unrelated lines.
Verified case 2026-07-20 (campaign-creation skill test_e2e.py): first patch call to add a try/except/else flag for the inline-format trigger regex produced mixed-indented Python inside extract_triggers_from_resolver. Pytest failed with AttributeError: 'NoneType' object has no attribute 'group' not because of logic, but because the early m_heading = re.search(...) line had been dedented to function-body level by an adjacent else: block, leaving the inner text = RESOLVER.read_text() line (originally inside the function) at a class-member indent. git diff revealed 12-space lines and 8-space lines interleaved inside the same function.
Fix recipes:
Rewrite the file with write_file whenever patch's old_string includes 5+ lines that all share indent. Don't try to surgically patch a multi-line indented block.
If you must use patch: pre-process old_string and new_string by counting shared leading whitespace and ensure the SURROUNDING context lines (before the block, after the block) are also present in BOTH strings with the SAME indentation as they appear on disk. The matcher anchors on those surrounding lines.
Validation step after every indented-block patch: run python3 -c "import ast; ast.parse(open('<file>').read())" to fail fast on IndentationError before pytest catches it indirectly.
# Verify Python syntax after a multi-line indented patch
python3 -c "import ast; ast.parse(open('~/.hermes/skills/<skill>/tests/test_e2e.py').read())" \
|| echo"INDENT CORRUPTED"
Cross-reference: Same trap family as Rule 1 (partial-read), Rule 4 (placeholder expansion), and Pitfall 1.2.0 (Mock attribute). The recurring lesson: when your mental model of indentation depth changes mid-patch, stop and rewrite.
Pitfall — patch reports success but disk content is unchanged (added 2026-08-01)
A different failure mode from the partial-read self-revert: the patch tool returns a successful ack (files_modified: [...]) and prints a clean unified diff in its response — but the file on disk was byte-identical before and after the call. Running git diff HEAD shows an empty diff, which proves the patch did NOT land, but it's easily misread as "the patch landed and produced zero changes" (which is its own bug class). The repeating trap is:
patch claims success and shows a diff
git status / git diff is clean (because the patch didn't write)
You commit, push, open PR — but the file you committed is the OLD file, because git add only sees the disk version (unchanged)
Or worse — the patched content was on disk transiently for some harness-internal state, the harness reverted it after the response was returned, and your subsequent read_file shows the original bytes
Verified case 2026-08-01, jleechanorg/user_scope PR #38 (cmux-resume-watchdog fix): I created a fresh worktree ~/.worktrees/user_scope-cmux-list-surfaces-fix off origin/main, then made two large patch calls — one to scripts/cmux_resume_watchdog.py (~91-line removal), one to tests/test_cmux_resume_watchdog.py (~168-line rewrite). Both returned files_modified ack with clean unified diffs. The live --scan-only smoke test passed (eligible=4 resumed=0), pytest tests/test_cmux_resume_watchdog.py showed 44/44 passed. I assumed the fix was live and committed/pushed/opened the PR. Reality: both files on disk were byte-identical to origin/main; the harness's patch tool had resolved the path against its main-worktree tracking rather than the new worktree path. The "44/44 passed" result was the OLD code being imported by pytest via the __pycache__ from a previous run that I had NOT cleared. The "live scan-only" output was from the OLD script. Net result: I was 5 minutes from merging dead PR when I happened to grep -c "def _list_workspace_terminal_surfaces" scripts/cmux_resume_watchdog.py and saw 2 (the dead function was still present) instead of 0 (which my patch should have produced). That grep saved it.
Trigger conditions to watch for (any one of these in the prior turn is a high-risk signal):
A freshly-created worktree (git worktree add ... origin/main) where files were loaded into the harness via terminal(grep ...) or execute_code(open(...).read()) rather than read_file(path, offset=1, limit=N) from the harness's own tool surface.
The patch call returns quickly with no warnings AND no obvious fuzzy-match evidence — meaning the resolution was against a stale model that conveniently happened to match.
git diff HEAD after the patch is empty (clean) when you expected +/- lines.
Stronger tripwires than git diff (since git diff lies about no-op in this case):
# Byte-count vs. expected (capture mtime + size BEFORE the patch as the baseline)stat -f "%N %z bytes %Sm" <file>
# patch…# After:stat -f "%N %z bytes %Sm" <file>
# Mismatch in size = patch didn't land.# Grep for a UNIQUE line from the new_string
grep -c "<unique sentinel from new_string>" <file>
# 0 = patch didn't land.# Re-read the file via read_file (harness-native), check the unique sentinel# is actually in the returned content.
Durable fix when this fires:
Stop patching; switch to write_file (full overwrite — works regardless of harness path resolution because the path is the same absolute path you pass in write_file's path parameter).
For complex multi-region edits, use execute_code with Python text replacement AND atomic os.replace:
import os, tempfile
fd, tmp = tempfile.mkstemp(dir=os.path.dirname(path), suffix='.py.tmp')
with os.fdopen(fd, 'w') as f:
f.write(new_content)
os.replace(tmp, path)
# Then verifyassert"expected sentinel"inopen(path).read()
write_file and execute_code both write to the explicit absolute path the harness passes them — neither has the stale-model-resolution bug that hit patch in the worktree case.
Cross-reference: Same trap family as Rule 1 (partial-read), Rule 3 (git diff tripwire), Pitfall 1.1.0 (3-retry loop), Pitfall 1.2.0 (Mock attribute), Pitfall 1.3.0 (string-presence assertion), Pitfall 1.4.0 (indented-block re-indentation). The recurring lesson: when the patch tool disagrees with disk reality, treat the tool's success report as suspect and verify with a fresh read.
