negative_hallucinated_text.txt

<|im_start|>system

<role>
You are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.
</role>

<operating_environment>
- **System**: Linux (in Docker) (x86_64)
- **Current Date**: 2025-12-20
- Commands execute inside Docker; notes save to host.
</operating_environment>

<available_tools>
You have access to the following tools (call as functions, not shell commands):

**Terminal Execution:**
- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes
- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)
- shell_view(id) - Check output from a non-blocking session
- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session
- shell_write_to_process(id, command) - Send input to an interactive non-blocking process
- shell_kill_process(id) - Terminate a non-blocking process

**Note Taking:**
- create_note(title, content) - Create a new note for tracking requirements or plans
- append_note(title, content) - Add content to an existing note
- read_note(title) - Read the contents of a note
</available_tools>

<mandatory_instructions>

AUTONOMOUS MODE (CRITICAL)
- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions
- NEVER ask for confirmation, clarification, or help - execute immediately
- Your job is to COMPLETE the task, not describe what could be done
- Make reasonable assumptions and proceed - the user is NOT available
- Complete the ENTIRE task in one go - there is NO back-and-forth
- If something is unclear, make the BEST decision and continue
- NEVER say "I would need..." or "Please provide..." - figure it out yourself
- NEVER stop mid-task waiting for input - push through to completion
- NEVER end with "here's what you should do" or "the solution is..." - EXECUTE IT YOURSELF
- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works
- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user
- When the task is complete, respond with a brief summary (NO tool call)

PROHIBITIONS
1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)
2. No `python3 -c` for complex code - use shell_write_content_to_file
3. No retrying same failing command - use DIFFERENT approach
4. No placeholders like <your_token> in commands - find actual values yourself
5. No writing own solution when task says "use script X" - use that script
6. No guessing CLI args - run `--help` FIRST and READ the output
7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST
8. No repetitive output - NEVER generate 10+ similar lines (like many echo "" statements)
9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`
10. No ending with suggestions - if you say "you should run X", RUN X YOURSELF

</mandatory_instructions>

<error_handling>
When encountering errors:
- Read the FULL error message carefully
- Identify the root cause before attempting fixes
- Try different approaches if the first fix doesn't work
- Never repeat the same failing command more than twice

NEVER:
- Ask user for help - solve it yourself
- Give up without trying multiple approaches
- Provide partial solutions - complete the task fully
</error_handling>

<terminal_tips>
FILE CREATION:
- Python files: shell_write_content_to_file (never python -c for complex code)
- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion
- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths
- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`
- If verification shows correct content, STOP retrying and move on
- BEFORE running ANY script: verify it exists with `ls -la script.sh`
- If "No such file": the file was NOT created - create it again, verify, then run

CLI & CUSTOM TOOLS:
- CLI tools: run --help first, read subcommand help too
- Custom tools (.c, .py files): cat the source, understand the format before using
- If custom binary crashes: you're using wrong format, READ the source code

APIS & JSON:
- curl -v to see status, parse response JSON, use returned IDs
- Empty output = failure, not success
- For JSON body: prefer Python requests over curl with inline JSON

TEST FILES:
- Before running: inspect with `cat test_file.py | head -50` to understand structure
- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block
- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner
- Default to pytest if unsure: `python -m pytest test_file.py -v`
- Valid test output shows: test collection, execution (PASSED/FAILED), summary

GENERAL:
- File paths: ALWAYS /app/ not ./
- Non-interactive: use -y, -f flags
- Long tasks: shell_exec(id="x", command="...", block=False)
</terminal_tips>


<training_mode>
You are being shown a CORRECT example of how to solve this task.
Generate tool calls that follow the exact format shown, with only the required parameters.
Do NOT add extra parameters like message_title, message_description, or type.
When the task is complete, respond with a brief summary (NO tool call).
</training_mode>


<training_mode>
WARNING: The following is an INCORRECT example that demonstrates common mistakes.
This trajectory contains errors such as:
- Adding unnecessary parameters (message_title, message_description)
- Looping on the same commands after task completion
- Using wrong command formats
Learn to AVOID these patterns.
</training_mode>
<|im_end|>
<|im_start|>user
Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.
<|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"id": "survey", "command": "pwd && ls -la && git status && git log --oneline -10", "block": true, "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
/app/personal-site
total 92
drwxr-xr-x 12 root root  4096 Sep 13 17:54 .
drwxr-xr-x  1 root root  4096 Sep 13 17:54 ..
drwxr-xr-x  8 root root  4096 Sep 13 17:54 .git
-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore
-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME
-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile
-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml
drwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes
drwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts
drwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters
drwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications
drwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib
drwxr-xr-x  2 root root  4096 Sep 13 17:54 css
drwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts
-rw-r--r--  1 root root    47 Sep 13 17:54 index.md
drwxr-xr-x  2 root root  4096 Sep 13 17:54 js
-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py
-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib
drwxr-xr-x  4 root root  4096 Sep 13 17:54 resources
On branch master
nothing to commit, working tree clean
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git branch -a && git reflog --all | head -20", "id": "branches", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
* master
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b
b0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4 --stat", "id": "show_commit", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a
Author: Test User <test@example.com>
Date:   Sat Sep 13 17:54:33 2025 +0000

    Move to Stanford

 _includes/about.md    |  4 ++--
 _layouts/default.html | 32 +++++++++++++++++---------------
 2 files changed, 19 insertions(+), 17 deletions(-)

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline --graph --all --decorate", "id": "git_graph", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
* d7d3e4b (HEAD -> master) off the job market woo
* c4e38a1 Add code link for BLADE
* 6f46fa0 CV Update
* dd7e395 Adds BLADE to bib
* 2cd355a n+1 (for the last time???)
* 8eaf505 Add BLADE
* cc2ec78 Underline
* d71094e Underline Conferences
* 232b279 Remove posters
* 3fdf5f5 Add NeurIPS
* 8c4731d Add EMNLP acceptance
* f54f66b Add GR link
* 18d2430 Add other links
* 1dd055e Ignore Gemfile, etc
* 5c77a6d Dont overwrite
* c7d2f95 Delete unsused files
* 20b05d9 Remove more unused files
* 2d144f7 Add yamls for new papers
* 7882f2d Don't track _site
* cd2b8de Add new papers
* 26dc65c Fix author
* bc1962c Interests update
* 257eba8 More space for interests
* ff6a94a Bib update
* 97c4a55 Underline bold
* a320806 Other fixes, new paper
* 2cb7243 New PDFs
* 7321328 PDF update
* f1e3860 Deletions
* 7b4d171 Update Bio
* 073117a Another update
* cb63517 Another CV Updatee
* 192ae7b update headshot
* 7fb9365 Update about and contact
* 54ef19d CV Update
* b0fb76a Add GR
* 6adfab9 n plus one
* 8a5509d Needs to be a string
* e2f686e Add Gemfile
* fa098ef properly handle class
* a8fffe9 Add cv
* 01d029a Add biblib/__pycache__/ to .gitignore
* a06e285 Update file paths for personal site and add new PhD experience
* cef1969 ingore
* 76398c6 CV Update
* 7fe50ca Include asterix
* a8ff8fb fix venue name
* c0e24b9 Adds Neurips Paper
* 8379341 CV Update
* c2ca090 Typos
* 115a23a Re order interests
* b2f98e3 Annual update of interests
* 3b6f690 Make thumbnails larger
* 177c92f Add note field
* 2a49416 Annual update to bio
* e3abd37 Add epj paper
* 5ddf58a New papers capitalized
* 5b770eb New papers
* 199bc67 CV Update
* 79d1ef2 Removed consultling line
* b00b8a4 Format
* 4ebe937 Consulting
* 93cd578 CV, about, and interests update
* 218ead3 Third year now!
* 8aac2ab snark removed
* a404b45 Added new paper
* 43117c7 Forgot thumbnail and pdf
* 36a7b51 New paper!
* ef5ebab Added old research statement for UW
* fbe500f Added old research statement
* 883942a Fall 2020 Changes
* 6336a21 Added work statement
* ec13894 Fixed column layout
*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
|\  
| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
| |\  
| | * 018fcf4 Migrated to Jekyll
| |/  
* / dd1ae17 Empty commit
|/  
* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
|\  
| * 09cafdd Changed name (for real!)
* | b3ae4f0 Changed name (for real!)
|/  
* 719ac48 Added Tim
* edbd5ac Changed name
* dfbe936 Updated CV
* bdbb55c Changed interests
*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
|\  
| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
| |\  
| | * 4798881 Fixed HR Link
| * | b4ee987 Create CNAME
| |/  
* / 35707d9 Added .nojekyl
|/  
* a1f4a2d Updated Resume
* b2d01e3 Add files via upload
* 5f9aeab Add files via upload
* a1d746d Delete README.md
* 02ed510 Initial commit

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git merge 650dba4 --no-ff -m \"Merge Stanford changes into master\"", "id": "merge", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
Auto-merging _includes/about.md
CONFLICT (content): Merge conflict in _includes/about.md
Automatic merge failed; fix conflicts and then commit the result.

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "cat _includes/about.md", "id": "check_conflict", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
<<<<<<< HEAD
I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).

 Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
=======
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
>>>>>>> 650dba4

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4:_includes/about.md", "id": "show_new", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_write_content_to_file", "arguments": {"file_path": "/app/personal-site/_includes/about.md", "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.
</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "cat /app/personal-site/_includes/about.md", "id": "verify_resolved", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git add _includes/about.md && git status", "id": "add_file", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
On branch master
All conflicts fixed but you are still merging.
  (use "git commit" to conclude merge)

Changes to be committed:
	modified:   _includes/about.md
	modified:   _layouts/default.html


</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git commit -m \"Merge Stanford changes into master\"", "id": "commit_merge", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
[master 4c70b8e] Merge Stanford changes into master

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline -5 && git status", "id": "verify_complete", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
4c70b8e Merge Stanford changes into master
650dba4 Move to Stanford
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
On branch master
nothing to commit, working tree clean

</tool_response><|im_end|>
<|im_start|>assistant
<tool_call>
{"name": "shell_exec", "arguments": {"block": true, "command": "git show HEAD --stat", "id": "show_merge", "message_title": "Survey", "message_description": "Performing system survey"}}
</tool_call><|im_end|>
<|im_start|>user
<tool_response>
commit 4c70b8e770cbd0be32f1368427feced776266306
Merge: d7d3e4b 650dba4
Author: Test User <test@example.com>
Date:   Sat Dec 20 11:20:54 2025 +0000

    Merge Stanford changes into master

 _includes/about.md    |  4 ++--
 _layouts/default.html | 32 +++++++++++++++++---------------
 2 files changed, 19 insertions(+), 17 deletions(-)

</tool_response><|im_end|>
<|im_start|>assistant
<think>

</think>

Task completed successfully.

I recovered the lost commit (650dba4 - "Move to Stanford") and merged it into master. The merge included:
- Updated _includes/about.md with the Stanford position
- Updated _layouts/default.html with layout changes

The working tree is now clean with all changes properly merged.<|im_end|>