From b5c6352587d6ad62e4f90821a468f1d06cc0af6d Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Tue, 23 Jun 2026 03:21:24 -0400
Subject: [PATCH 1/9] Don't yap for the LLM

---
 cecli/helpers/conversation/files.py       | 14 ----
 cecli/helpers/conversation/integration.py | 85 +----------------------
 2 files changed, 2 insertions(+), 97 deletions(-)

diff --git a/cecli/helpers/conversation/files.py b/cecli/helpers/conversation/files.py
index 8b703e674ae..78eee14028f 100644
--- a/cecli/helpers/conversation/files.py
+++ b/cecli/helpers/conversation/files.py
@@ -289,26 +289,12 @@ def update_file_diff(self, fname: str) -> Optional[str]:
                 ),
             }
 
-            assistant_msg = {
-                "role": "assistant",
-                "content": (
-                    f"Thank you for sharing this {prefix_str}diff of the updates to {rel_fname}."
-                    " I will review their contents."
-                ),
-            }
-
             ConversationService.get_manager(coder).add_message(
                 message_dict=diff_message,
                 tag=MessageTag.DIFFS,
                 hash_key=("file_diff_user", rel_fname, content_hash),
             )
 
-            ConversationService.get_manager(coder).add_message(
-                message_dict=assistant_msg,
-                tag=MessageTag.DIFFS,
-                hash_key=("file_diff_assistant", rel_fname, content_hash),
-            )
-
         return diff
 
     def get_file_stub(self, fname: str) -> str:
diff --git a/cecli/helpers/conversation/integration.py b/cecli/helpers/conversation/integration.py
index a9381d4ecbb..da52ec5e6a6 100644
--- a/cecli/helpers/conversation/integration.py
+++ b/cecli/helpers/conversation/integration.py
@@ -527,10 +527,6 @@ def add_repo_map_messages(self) -> List[Dict[str, Any]]:
             # Create repository map messages
             dict_repo_messages = [
                 dict(role="user", content=repo_content),
-                dict(
-                    role="assistant",
-                    content="Thank you, these files will help with navigating the codebase.",
-                ),
             ]
 
             # Add messages to conversation manager with appropriate priority
@@ -579,11 +575,6 @@ def add_rules_messages(self) -> List[Dict[str, Any]]:
                 "role": "user",
                 "content": f"Rules defined in {rel_fname}:\n\n{content}",
             }
-            # Create assistant message
-            assistant_msg = {
-                "role": "assistant",
-                "content": f"I understand the rules in {rel_fname} and will follow them.",
-            }
 
             # Add to ConversationManager with RULES tag
             ConversationService.get_manager(coder).add_message(
@@ -594,15 +585,7 @@ def add_rules_messages(self) -> List[Dict[str, Any]]:
                 update_timestamp=False,
             )
 
-            ConversationService.get_manager(coder).add_message(
-                message_dict=assistant_msg,
-                tag=MessageTag.RULES,
-                hash_key=("rules_assistant", fname),
-                force=True,
-                update_timestamp=False,
-            )
-
-            messages.extend([user_msg, assistant_msg])
+            messages.extend([user_msg])
 
         return messages
 
@@ -667,20 +650,6 @@ def add_readonly_files_messages(self) -> List[Dict[str, Any]]:
                 )
                 messages.append(user_msg)
 
-                # Add assistant message with file path as hash_key
-                assistant_msg = {
-                    "role": "assistant",
-                    "content": f"Thank you for sharing the file contents for {rel_fname}.",
-                }
-                ConversationService.get_manager(coder).add_message(
-                    message_dict=assistant_msg,
-                    tag=MessageTag.READONLY_FILES,
-                    hash_key=("file_assistant", fname),  # Use file path as part of hash_key
-                    force=True,
-                    update_timestamp=False,
-                )
-                messages.append(assistant_msg)
-
             # Check if file has changed and add diff message if needed
             if ConversationService.get_files(coder).has_file_changed(fname):
                 ConversationService.get_files(coder).update_file_diff(fname)
@@ -692,13 +661,6 @@ def add_readonly_files_messages(self) -> List[Dict[str, Any]]:
                 # Add individual image message to result
                 messages.append(img_msg)
 
-                # Add individual assistant acknowledgment for each image
-                assistant_msg = {
-                    "role": "assistant",
-                    "content": "Ok, I will use this image as a reference.",
-                }
-                messages.append(assistant_msg)
-
                 # Get the file name from the message (stored in image_file key)
                 fname = img_msg.get("image_file")
                 if fname:
@@ -708,11 +670,6 @@ def add_readonly_files_messages(self) -> List[Dict[str, Any]]:
                         tag=MessageTag.READONLY_FILES,
                         hash_key=("image_user", fname),
                     )
-                    ConversationService.get_manager(coder).add_message(
-                        message_dict=assistant_msg,
-                        tag=MessageTag.READONLY_FILES,
-                        hash_key=("image_assistant", fname),
-                    )
 
         return messages
 
@@ -767,15 +724,9 @@ def add_chat_files_messages(self) -> Dict[str, Any]:
                 "content": f"{file_preamble}\n{rel_fname}\n\n{content}\n\n{file_postamble}",
             }
 
-            # Create assistant message
-            assistant_msg = {
-                "role": "assistant",
-                "content": f"Thank you for sharing the file contents for {rel_fname}.",
-            }
-
             # Determine tag based on editability
             tag = MessageTag.CHAT_FILES
-            result["chat_files"].extend([user_msg, assistant_msg])
+            result["chat_files"].extend([user_msg])
 
             # Add user message to ConversationManager with file path as hash_key
             ConversationService.get_manager(coder).add_message(
@@ -786,15 +737,6 @@ def add_chat_files_messages(self) -> Dict[str, Any]:
                 update_timestamp=False,
             )
 
-            # Add assistant message to ConversationManager with file path as hash_key
-            ConversationService.get_manager(coder).add_message(
-                message_dict=assistant_msg,
-                tag=tag,
-                hash_key=("file_assistant", fname),  # Use file path as part of hash_key
-                force=True,
-                update_timestamp=False,
-            )
-
             # Check if file has changed and add diff message if needed
             if ConversationService.get_files(coder).has_file_changed(fname):
                 ConversationService.get_files(coder).update_file_diff(fname)
@@ -806,13 +748,6 @@ def add_chat_files_messages(self) -> Dict[str, Any]:
                 # Add individual image message to result
                 result["chat_files"].append(img_msg)
 
-                # Add individual assistant acknowledgment for each image
-                assistant_msg = {
-                    "role": "assistant",
-                    "content": "Ok, I will use this image as a reference.",
-                }
-                result["chat_files"].append(assistant_msg)
-
                 # Get the file name from the message (stored in image_file key)
                 fname = img_msg.get("image_file")
                 if fname:
@@ -822,11 +757,6 @@ def add_chat_files_messages(self) -> Dict[str, Any]:
                         tag=MessageTag.CHAT_FILES,
                         hash_key=("image_user", fname),
                     )
-                    ConversationService.get_manager(coder).add_message(
-                        message_dict=assistant_msg,
-                        tag=MessageTag.CHAT_FILES,
-                        hash_key=("image_assistant", fname),
-                    )
 
         return result
 
@@ -858,11 +788,6 @@ def add_file_context_messages(self, promote_messages=True) -> None:
                 "content": f"ID-Prefixed Context For:\n{rel_fname}\n\n{context_content}",
             }
 
-            assistant_msg = {
-                "role": "assistant",
-                "content": f"Thank you for sharing the prefixed file contents for {rel_fname}.",
-            }
-
             # Add to conversation manager
             content_hash = xxhash.xxh3_128_hexdigest(context_content.encode("utf-8"))
             ConversationService.get_manager(coder).queue_message(
@@ -871,12 +796,6 @@ def add_file_context_messages(self, promote_messages=True) -> None:
                 hash_key=("file_context_user", file_path, content_hash),
             )
 
-            ConversationService.get_manager(coder).queue_message(
-                message_dict=assistant_msg,
-                tag=MessageTag.FILE_CONTEXTS,
-                hash_key=("file_context_assistant", file_path, content_hash),
-            )
-
     def reset(self) -> None:
         """
         Reset the entire conversation system to initial state.

From 857cf690fb58c87bf75b6525d072cbef246dea21 Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Tue, 23 Jun 2026 03:32:57 -0400
Subject: [PATCH 2/9] Update repo links in docs

---
 cecli/coders/base_coder.py                    |  3 +-
 cecli/urls.py                                 |  8 ++--
 cecli/versioncheck.py                         |  2 +-
 cecli/website/_config.yml                     |  4 +-
 cecli/website/_includes/help.md               |  2 +-
 cecli/website/docs/benchmarks-1106.md         |  2 +-
 cecli/website/docs/benchmarks-speed-1106.md   |  2 +-
 cecli/website/docs/benchmarks.md              |  8 ++--
 .../website/docs/config/adv-model-settings.md |  2 +-
 cecli/website/docs/config/agent-mode.md       |  2 +-
 .../docs/config/{aider_conf.md => conf.md}    | 37 +------------------
 cecli/website/docs/config/dotenv.md           |  2 +-
 cecli/website/docs/config/reasoning.md        |  2 +-
 cecli/website/docs/ctags.md                   |  4 +-
 cecli/website/docs/git.md                     |  2 +-
 cecli/website/docs/languages.md               |  2 +-
 cecli/website/docs/leaderboards/contrib.md    |  4 +-
 cecli/website/docs/leaderboards/edit.md       |  4 +-
 cecli/website/docs/more/analytics.md          |  4 +-
 cecli/website/docs/repomap.md                 |  4 +-
 cecli/website/docs/scripting.md               |  2 +-
 cecli/website/docs/troubleshooting/imports.md |  2 +-
 cecli/website/docs/unified-diffs.md           |  2 +-
 cecli/website/docs/usage/optional.md          |  2 +-
 24 files changed, 35 insertions(+), 73 deletions(-)
 rename cecli/website/docs/config/{aider_conf.md => conf.md} (92%)

diff --git a/cecli/coders/base_coder.py b/cecli/coders/base_coder.py
index ceeb4862a3d..bb677a15e68 100755
--- a/cecli/coders/base_coder.py
+++ b/cecli/coders/base_coder.py
@@ -876,9 +876,8 @@ def get_announcements(self):
             env_items.append(f"{rel_repo_dir} ({num_files:,} files)")
             if num_files > 1000:
                 env_items.append(
-                    "Warning: For large repos, consider using --subtree-only and .cecli_ignore"
+                    "Warning: For large repos, consider using --subtree-only and .cecli.ignore"
                 )
-                env_items.append(f"See: {urls.large_repos}")
         else:
             env_items.append("no git repo")
 
diff --git a/cecli/urls.py b/cecli/urls.py
index d2e30182dc9..9a5c44c0593 100644
--- a/cecli/urls.py
+++ b/cecli/urls.py
@@ -1,16 +1,14 @@
 website = "https://cecli.dev/"
-add_all_files = "https://cecli.dev/docs/faq.html#how-can-i-add-all-the-files-to-the-chat"
 edit_errors = "https://cecli.dev/docs/troubleshooting/edit-errors.html"
 git = "https://cecli.dev/docs/git.html"
-enable_playwright = "https://cecli.dev/docs/install/optional.html#enable-playwright"
+enable_playwright = "https://cecli.dev/docs/usage/optional.html#enable-playwright"
 favicon = "https://cecli.dev/assets/cecli-temp-logo-favicon.svg"
 model_warnings = "https://cecli.dev/docs/llms/warnings.html"
 token_limits = "https://cecli.dev/docs/troubleshooting/token-limits.html"
 llms = "https://cecli.dev/docs/llms.html"
-large_repos = "https://cecli.dev/docs/faq.html#can-i-use-cecli-in-a-large-mono-repo"
-github_issues = "https://github.com/dwash96/cecli/issues/new"
+github_issues = "https://github.com/cecli-dev/cecli/issues/new"
 git_index_version = "https://github.com/Aider-AI/aider/issues/211"
 install_properly = "https://cecli.dev/docs/troubleshooting/imports.html"
-release_notes = "https://github.com/dwash96/cecli/releases/latest"
+release_notes = "https://github.com/cecli-dev/cecli/releases/latest"
 edit_formats = "https://cecli.dev/docs/more/edit-formats.html"
 models_and_keys = "https://cecli.dev/docs/troubleshooting/models-and-keys.html"
diff --git a/cecli/versioncheck.py b/cecli/versioncheck.py
index 05d13fe964f..95ff02b32b7 100644
--- a/cecli/versioncheck.py
+++ b/cecli/versioncheck.py
@@ -21,7 +21,7 @@ async def install_from_main_branch(io):
         io,
         None,
         "Install the development version of cecli from the main branch?",
-        ["git+https://github.com/dwash96/cecli.git"],
+        ["git+https://github.com/cecli-dev/cecli.git"],
         self_update=True,
     )
 
diff --git a/cecli/website/_config.yml b/cecli/website/_config.yml
index f88ca4c1b1f..5b664e866ae 100644
--- a/cecli/website/_config.yml
+++ b/cecli/website/_config.yml
@@ -24,7 +24,7 @@ exclude:
 
 aux_links:
   "GitHub":
-    - "https://github.com/dwash96/cecli"
+    - "https://github.com/cecli-dev/cecli"
   "Discord":
     - "https://discord.gg/AX9ZEA7nJn"
   "Support":
@@ -32,7 +32,7 @@ aux_links:
 
 nav_external_links:
   - title: "GitHub"
-    url: "https://github.com/dwash96/cecli"
+    url: "https://github.com/cecli-dev/cecli"
   - title: "Discord"
     url: "https://discord.gg/AX9ZEA7nJn"
   - title: "Support"
diff --git a/cecli/website/_includes/help.md b/cecli/website/_includes/help.md
index 89955bac765..2999741f739 100644
--- a/cecli/website/_includes/help.md
+++ b/cecli/website/_includes/help.md
@@ -1,5 +1,5 @@
 If you need more help, please check our
-[GitHub issues](https://github.com/dwash96/cecli/issues)
+[GitHub issues](https://github.com/cecli-dev/cecli/issues)
 and file a new issue if your problem isn't discussed.
 Or drop into our
 [Discord](https://discord.gg/g4bF53fSWF)
diff --git a/cecli/website/docs/benchmarks-1106.md b/cecli/website/docs/benchmarks-1106.md
index 1555ef3bd55..a66892d1351 100644
--- a/cecli/website/docs/benchmarks-1106.md
+++ b/cecli/website/docs/benchmarks-1106.md
@@ -19,7 +19,7 @@ and there's a lot
 of interest about their ability to code compared to the previous versions.
 With that in mind, I've been benchmarking the new models.
 
-[cecli](https://github.com/dwash96/cecli)
+[cecli](https://github.com/cecli-dev/cecli)
 is an open source command line chat tool that lets you work with GPT to edit
 code in your local git repo.
 To do this, cecli needs to be able to reliably recognize when GPT wants to edit
diff --git a/cecli/website/docs/benchmarks-speed-1106.md b/cecli/website/docs/benchmarks-speed-1106.md
index 36c3edd8c52..db91a9e7959 100644
--- a/cecli/website/docs/benchmarks-speed-1106.md
+++ b/cecli/website/docs/benchmarks-speed-1106.md
@@ -20,7 +20,7 @@ and there's a lot
 of interest about their capabilities and performance.
 With that in mind, I've been benchmarking the new models.
 
-[cecli](https://github.com/dwash96/cecli)
+[cecli](https://github.com/cecli-dev/cecli)
 is an open source command line chat tool that lets you work with GPT to edit
 code in your local git repo.
 cecli relies on a
diff --git a/cecli/website/docs/benchmarks.md b/cecli/website/docs/benchmarks.md
index 108cc67ca3c..8226a276266 100644
--- a/cecli/website/docs/benchmarks.md
+++ b/cecli/website/docs/benchmarks.md
@@ -168,7 +168,7 @@ requests:
 ### whole
 
 The
-[whole](https://github.com/dwash96/cecli/blob/main/cecli/coders/wholefile_prompts.py)
+[whole](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/wholefile_prompts.py)
 format asks GPT to return an updated copy of the entire file, including any changes.
 The file should be
 formatted with normal markdown triple-backtick fences, inlined with the rest of its response text.
@@ -187,7 +187,7 @@ def main():
 
 ### diff
 
-The [diff](https://github.com/dwash96/cecli/blob/main/cecli/coders/editblock_prompts.py)
+The [diff](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/editblock_prompts.py)
 format also asks GPT to return edits as part of the normal response text,
 in a simple diff format.
 Each edit is a fenced code block that
@@ -209,7 +209,7 @@ demo.py
 
 ### whole-func
 
-The [whole-func](https://github.com/dwash96/cecli/blob/main/cecli/coders/wholefile_func_coder.py)
+The [whole-func](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/wholefile_func_coder.py)
 format requests updated copies of whole files to be returned using the function call API.
 
 
@@ -227,7 +227,7 @@ format requests updated copies of whole files to be returned using the function
 ### diff-func
 
 The
-[diff-func](https://github.com/dwash96/cecli/blob/main/cecli/coders/editblock_func_coder.py)
+[diff-func](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/editblock_func_coder.py)
 format requests a list of
 original/updated style edits to be returned using the function call API.
 
diff --git a/cecli/website/docs/config/adv-model-settings.md b/cecli/website/docs/config/adv-model-settings.md
index a96d8b80cbd..e2d4c6c5997 100644
--- a/cecli/website/docs/config/adv-model-settings.md
+++ b/cecli/website/docs/config/adv-model-settings.md
@@ -122,7 +122,7 @@ These settings will be merged with any model-specific settings, with the
 Below are all the pre-configured model settings to give a sense for the settings which are supported.
 
 You can also look at the `ModelSettings` class in
-[models.py](https://github.com/dwash96/cecli/blob/main/cecli/models.py)
+[models.py](https://github.com/cecli-dev/cecli/blob/main/cecli/models.py)
 file for more details about all of the model setting that cecli supports.
 
 The first entry shows all the settings, with their default values.
diff --git a/cecli/website/docs/config/agent-mode.md b/cecli/website/docs/config/agent-mode.md
index f0d7e01fa02..5f3f69af14d 100644
--- a/cecli/website/docs/config/agent-mode.md
+++ b/cecli/website/docs/config/agent-mode.md
@@ -306,7 +306,7 @@ agent-config:
   skills_init: ["python-refactoring"]
 ```
 
-For complete documentation on creating and using skills, including skill directory structure, SKILL.md format, and best practices, see the [Skills documentation](https://github.com/dwash96/cecli/blob/main/cecli/website/docs/config/skills.md).
+For complete documentation on creating and using skills, including skill directory structure, SKILL.md format, and best practices, see the [Skills documentation](https://github.com/cecli-dev/cecli/blob/main/cecli/website/docs/config/skills.md).
 
 ### Benefits
 - **Autonomous operation**: Reduces need for manual file management
diff --git a/cecli/website/docs/config/aider_conf.md b/cecli/website/docs/config/conf.md
similarity index 92%
rename from cecli/website/docs/config/aider_conf.md
rename to cecli/website/docs/config/conf.md
index b4d0c31aa47..efcb199eb1e 100644
--- a/cecli/website/docs/config/aider_conf.md
+++ b/cecli/website/docs/config/conf.md
@@ -40,7 +40,7 @@ read: [CONVENTIONS.md, anotherfile.txt, thirdfile.py]
 
 Below is a sample of the YAML config file, which you
 can also
-[download from GitHub](https://github.com/dwash96/cecli/blob/main/cecli/website/assets/sample.cecli.conf.yml).
+[download from GitHub](https://github.com/cecli-dev/cecli/blob/main/cecli/website/assets/sample.cecli.conf.yml).
 
 <!--[[[cog
 from cecli.args import get_sample_yaml
@@ -506,40 +506,5 @@ cog.outl("```")
 ## Print shell completion script for the specified SHELL and exit. Supported shells: bash, tcsh, zsh. Example: cecli --shell-completions bash
 #shell-completions: xxx
 
-############################
-# Deprecated model settings:
-
-## Use claude-3-opus-20240229 model for the main chat (deprecated, use --model)
-#opus: false
-
-## Use anthropic/claude-3-7-sonnet-20250219 model for the main chat (deprecated, use --model)
-#sonnet: false
-
-## Use claude-3-5-haiku-20241022 model for the main chat (deprecated, use --model)
-#haiku: false
-
-## Use gpt-4-0613 model for the main chat (deprecated, use --model)
-#4: false
-
-## Use gpt-4o model for the main chat (deprecated, use --model)
-#4o: false
-
-## Use gpt-4o-mini model for the main chat (deprecated, use --model)
-#mini: false
-
-## Use gpt-4-1106-preview model for the main chat (deprecated, use --model)
-#4-turbo: false
-
-## Use gpt-3.5-turbo model for the main chat (deprecated, use --model)
-#35turbo: false
-
-## Use deepseek/deepseek-chat model for the main chat (deprecated, use --model)
-#deepseek: false
-
-## Use o1-mini model for the main chat (deprecated, use --model)
-#o1-mini: false
-
-## Use o1-preview model for the main chat (deprecated, use --model)
-#o1-preview: false
 ```
 <!--[[[end]]]-->
diff --git a/cecli/website/docs/config/dotenv.md b/cecli/website/docs/config/dotenv.md
index 089b02c9a17..f987d477701 100644
--- a/cecli/website/docs/config/dotenv.md
+++ b/cecli/website/docs/config/dotenv.md
@@ -26,7 +26,7 @@ If the files above exist, they will be loaded in that order. Files loaded last w
 
 Below is a sample `.env` file, which you
 can also
-[download from GitHub](https://github.com/dwash96/cecli/blob/main/cecli/website/assets/sample.env).
+[download from GitHub](https://github.com/cecli-dev/cecli/blob/main/cecli/website/assets/sample.env).
 
 <!--[[[cog
 from cecli.args import get_sample_dotenv
diff --git a/cecli/website/docs/config/reasoning.md b/cecli/website/docs/config/reasoning.md
index b12ecd80944..1aa30e8ce82 100644
--- a/cecli/website/docs/config/reasoning.md
+++ b/cecli/website/docs/config/reasoning.md
@@ -170,7 +170,7 @@ Reasoning models often have specific requirements for these settings:
 | `use_system_prompt` | Whether to use system prompt | Some reasoning models don't support system prompts |
 
 It may be helpful to find one of the 
-[existing model setting configuration entries](https://github.com/dwash96/cecli/blob/main/cecli/resources/model-settings.yml)
+[existing model setting configuration entries](https://github.com/cecli-dev/cecli/blob/main/cecli/resources/model-settings.yml)
 for the model you are interested in, say o3-mini:
 
 ```yaml
diff --git a/cecli/website/docs/ctags.md b/cecli/website/docs/ctags.md
index e49c187a56c..1d37ed58b48 100644
--- a/cecli/website/docs/ctags.md
+++ b/cecli/website/docs/ctags.md
@@ -112,9 +112,9 @@ like functions and methods also include their signatures.
 
 Here's a
 sample of the map of the cecli repo, just showing the maps of
-[main.py](https://github.com/dwash96/cecli/blob/main/cecli/main.py)
+[main.py](https://github.com/cecli-dev/cecli/blob/main/cecli/main.py)
 and
-[io.py](https://github.com/dwash96/cecli/blob/main/cecli/io.py)
+[io.py](https://github.com/cecli-dev/cecli/blob/main/cecli/io.py)
 :
 
 ```
diff --git a/cecli/website/docs/git.md b/cecli/website/docs/git.md
index 93a1ff6fa67..fab890975cf 100644
--- a/cecli/website/docs/git.md
+++ b/cecli/website/docs/git.md
@@ -50,7 +50,7 @@ By default, cecli creates commit messages which follow
 [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/).
 
 You can customize the
-[commit prompt](https://github.com/dwash96/cecli/blob/main/cecli/prompts.py#L5)
+[commit prompt](https://github.com/cecli-dev/cecli/blob/main/cecli/prompts.py#L5)
 with the `--commit-prompt` option.
 You can place that on the command line, or 
 [configure it via a config file or environment variables](https://cecli.dev/docs/config.html).
diff --git a/cecli/website/docs/languages.md b/cecli/website/docs/languages.md
index ca23bd6a126..07664728c97 100644
--- a/cecli/website/docs/languages.md
+++ b/cecli/website/docs/languages.md
@@ -33,7 +33,7 @@ then it should be possible to add repo map support.
 To build a repo map, cecli needs the `tags.scm` file
 from the given language's tree-sitter grammar.
 If you can find and share that file in a 
-[GitHub issue](https://github.com/dwash96/cecli/issues),
+[GitHub issue](https://github.com/cecli-dev/cecli/issues),
 then it may be possible to add repo map support.
 
 If cecli doesn't already support linting your language, 
diff --git a/cecli/website/docs/leaderboards/contrib.md b/cecli/website/docs/leaderboards/contrib.md
index 63763765b87..fbf7f336388 100644
--- a/cecli/website/docs/leaderboards/contrib.md
+++ b/cecli/website/docs/leaderboards/contrib.md
@@ -7,8 +7,8 @@ nav_order: 900
 
 Contributions of benchmark results are welcome!
 See the
-[benchmark README](https://github.com/dwash96/cecli/blob/main/benchmark/README.md)
+[benchmark README](https://github.com/cecli-dev/cecli/blob/main/benchmark/README.md)
 for information on running cecli's code editing benchmarks.
 Submit results by opening a PR with edits to the
-[benchmark results data files](https://github.com/dwash96/cecli/blob/main/cecli/website/_data/).
+[benchmark results data files](https://github.com/cecli-dev/cecli/blob/main/cecli/website/_data/).
 
diff --git a/cecli/website/docs/leaderboards/edit.md b/cecli/website/docs/leaderboards/edit.md
index 434b6f16a63..1b1f5b3a459 100644
--- a/cecli/website/docs/leaderboards/edit.md
+++ b/cecli/website/docs/leaderboards/edit.md
@@ -99,10 +99,10 @@ since it is the easiest format for an LLM to use.
 
 Contributions of benchmark results are welcome!
 See the
-[benchmark README](https://github.com/dwash96/cecli/blob/main/benchmark/README.md)
+[benchmark README](https://github.com/cecli-dev/cecli/blob/main/benchmark/README.md)
 for information on running cecli's code editing benchmarks.
 Submit results by opening a PR with edits to the
-[benchmark results data files](https://github.com/dwash96/cecli/blob/main/cecli/website/_data/).
+[benchmark results data files](https://github.com/cecli-dev/cecli/blob/main/cecli/website/_data/).
 
 
 <p class="post-date">
diff --git a/cecli/website/docs/more/analytics.md b/cecli/website/docs/more/analytics.md
index 8b4bf2cb098..2670eefeb97 100644
--- a/cecli/website/docs/more/analytics.md
+++ b/cecli/website/docs/more/analytics.md
@@ -77,7 +77,7 @@ If you say "no", analytics will be permanently disabled.
 ### Sample analytics data
 
 To get a better sense of what type of data is collected, you can review some
-[sample analytics logs](https://github.com/dwash96/cecli/blob/main/cecli/website/assets/sample-analytics.jsonl).
+[sample analytics logs](https://github.com/cecli-dev/cecli/blob/main/cecli/website/assets/sample-analytics.jsonl).
 These are the last 1,000 analytics events from the author's
 personal use of cecli, updated regularly.
 
@@ -117,7 +117,7 @@ cecli uses PostHog for analytics collection. You can configure cecli to send ana
 If you have concerns about any of the analytics that cecli is collecting
 or our data practices
 please contact us by opening a
-[GitHub Issue](https://github.com/dwash96/cecli/issues).
+[GitHub Issue](https://github.com/cecli-dev/cecli/issues).
 
 ## Privacy policy
 
diff --git a/cecli/website/docs/repomap.md b/cecli/website/docs/repomap.md
index c05d47360e8..67ea8bc75aa 100644
--- a/cecli/website/docs/repomap.md
+++ b/cecli/website/docs/repomap.md
@@ -29,9 +29,9 @@ It shows how each of these symbols are defined, by including the critical lines
 
 Here's a part of
 the repo map of cecli's repo, for
-[base_coder.py](https://github.com/dwash96/cecli/blob/main/cecli/coders/base_coder.py)
+[base_coder.py](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/base_coder.py)
 and
-[commands.py](https://github.com/dwash96/cecli/blob/main/cecli/commands.py)
+[commands.py](https://github.com/cecli-dev/cecli/blob/main/cecli/commands.py)
 :
 
 ```
diff --git a/cecli/website/docs/scripting.md b/cecli/website/docs/scripting.md
index de2d6f95de7..6be657fde2f 100644
--- a/cecli/website/docs/scripting.md
+++ b/cecli/website/docs/scripting.md
@@ -83,7 +83,7 @@ coder.run("/tokens")
 ```
 
 See the
-[Coder.create() and Coder.__init__() methods](https://github.com/dwash96/cecli/blob/main/cecli/coders/base_coder.py)
+[Coder.create() and Coder.__init__() methods](https://github.com/cecli-dev/cecli/blob/main/cecli/coders/base_coder.py)
 for all the supported arguments.
 
 It can also be helpful to set the equivalent of `--yes` by doing this:
diff --git a/cecli/website/docs/troubleshooting/imports.md b/cecli/website/docs/troubleshooting/imports.md
index f7028508321..271bd4b55b5 100644
--- a/cecli/website/docs/troubleshooting/imports.md
+++ b/cecli/website/docs/troubleshooting/imports.md
@@ -50,7 +50,7 @@ cecli uses.
 
 In particular, be careful with the packages with pinned versions 
 noted at the end of
-[cecli's requirements.in file](https://github.com/dwash96/cecli/blob/main/requirements/requirements.in).
+[cecli's requirements.in file](https://github.com/cecli-dev/cecli/blob/main/requirements/requirements.in).
 These versions are pinned because cecli is known not to work with the
 latest versions of these libraries.
 
diff --git a/cecli/website/docs/unified-diffs.md b/cecli/website/docs/unified-diffs.md
index f9af0f53bb5..cf8e046206a 100644
--- a/cecli/website/docs/unified-diffs.md
+++ b/cecli/website/docs/unified-diffs.md
@@ -332,7 +332,7 @@ where we ask GPT to do something like:
 > Name the new function `_set_csrf_cookie`, exactly the same name as the existing method.
 > Update any existing `self._set_csrf_cookie` calls to work with the new `_set_csrf_cookie` function.
 
-A [simple python AST scanning script](https://github.com/dwash96/cecli/blob/main/benchmark/refactor_tools.py)
+A [simple python AST scanning script](https://github.com/cecli-dev/cecli/blob/main/benchmark/refactor_tools.py)
 found 89 suitable files
 and packaged them up as benchmark tasks.
 Each task has a test
diff --git a/cecli/website/docs/usage/optional.md b/cecli/website/docs/usage/optional.md
index 6aa97e574cd..2bcce8a9501 100644
--- a/cecli/website/docs/usage/optional.md
+++ b/cecli/website/docs/usage/optional.md
@@ -95,6 +95,6 @@ There are a number of 3rd party
 
 If you are interested in creating an cecli plugin for your favorite editor,
 please let us know by opening a
-[GitHub issue](https://github.com/dwash96/cecli/issues).
+[GitHub issue](https://github.com/cecli-dev/cecli/issues).
 
 

From 0bbb611c7e4d46cb8d969f6a418461a5b4c0ec4e Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Wed, 24 Jun 2026 08:54:35 -0400
Subject: [PATCH 3/9] Improve stdin propagation to background commands

---
 cecli/coders/agent_coder.py          |   5 +
 cecli/helpers/background_commands.py | 171 +++++++++++++++++----
 cecli/tools/command.py               | 215 ++++++++++++++++++---------
 3 files changed, 291 insertions(+), 100 deletions(-)

diff --git a/cecli/coders/agent_coder.py b/cecli/coders/agent_coder.py
index 94d61738442..c58ffb8da32 100644
--- a/cecli/coders/agent_coder.py
+++ b/cecli/coders/agent_coder.py
@@ -1666,6 +1666,11 @@ def get_background_command_output(self):
                 command_str = command_info.get(command_key, {}).get("command", command_key)
                 output += f"\n[bg: {command_str}]\n{cmd_output}\n"
 
+        # Clean up stale (finished) background commands after reading their output
+        for command_key, info in command_info.items():
+            if not info.get("running", False):
+                BackgroundCommandManager.stop_background_command(command_key)
+
         return output
 
     def get_git_status(self):
diff --git a/cecli/helpers/background_commands.py b/cecli/helpers/background_commands.py
index 2789fec0ebc..825dd09ad50 100644
--- a/cecli/helpers/background_commands.py
+++ b/cecli/helpers/background_commands.py
@@ -5,7 +5,6 @@
 in the background and capturing their output for injection into chat streams.
 """
 
-import codecs
 import os
 import platform
 import subprocess
@@ -171,31 +170,86 @@ def _start_output_reader(self) -> None:
         """Start thread to read process output."""
 
         def reader():
-            try:
-                # Simple approach: read lines when available
-                # This will block on readline(), but that's OK because
-                # we're in a separate thread and the buffer will capture
-                # output as soon as it's available
+            import re
+
+            # Regex to strip ANSI terminal escape sequences
+            _ansi_escape = re.compile(
+                r"\x1b\[[0-9;]*[a-zA-Z]|\x1b[\]^_]|[\x1b\x9b][][()#;?]*"
+                r"(?:[0-9]{1,4}(?:;[0-9]{0,4})*)?[0-9A-PRZcf-nqry=><~]"
+            )
 
+            def _strip_ansi(text: str) -> str:
+                return _ansi_escape.sub("", text)
+
+            try:
                 if self.master_fd is not None:
                     while not self._stop_event.is_set():
                         try:
                             data = os.read(self.master_fd, 4096).decode(errors="replace")
                             if not data:
                                 break
-                            self.buffer.append(data)
+                            # Strip ANSI escape sequences from PTY output
+                            self.buffer.append(_strip_ansi(data))
                         except (OSError, EOFError):
                             break
                 else:
-                    # Read stdout
-                    for line in iter(self.process.stdout.readline, ""):
-                        if line:
-                            self.buffer.append(line)
+                    has_stdout_fileno = hasattr(self.process.stdout, "fileno")
+                    if has_stdout_fileno:
+                        os.set_blocking(self.process.stdout.fileno(), False)
+                    while not self._stop_event.is_set():
+                        try:
+                            if has_stdout_fileno:
+                                # Use os.read() instead of readline() to capture
+                                # partial line output (e.g. REPL prompts without newlines)
+                                data = os.read(self.process.stdout.fileno(), 4096).decode(
+                                    errors="replace"
+                                )
+                            else:
+                                # Fallback to readline when fileno() is unavailable
+                                # (e.g. mock objects in tests)
+                                data = self.process.stdout.readline()
+                            if data:
+                                self.buffer.append(data)
+                            else:
+                                # Check if process died
+                                if not self.is_alive():
+                                    if has_stdout_fileno:
+                                        # Read any remaining data
+                                        try:
+                                            remaining = os.read(
+                                                self.process.stdout.fileno(), 4096
+                                            ).decode(errors="replace")
+                                            if remaining:
+                                                self.buffer.append(remaining)
+                                        except (OSError, EOFError):
+                                            pass
+                                    break
+                                import time
+
+                                time.sleep(0.05)
+                        except (OSError, EOFError, ValueError):
+                            if not self.is_alive():
+                                break
+                            import time
+
+                            time.sleep(0.05)
 
-                    # Read stderr
-                    for line in iter(self.process.stderr.readline, ""):
-                        if line:
-                            self.buffer.append(line)
+                    # Also capture stderr (best-effort, non-blocking)
+                    if hasattr(self.process.stderr, "fileno"):
+                        try:
+                            os.set_blocking(self.process.stderr.fileno(), False)
+                            while True:
+                                try:
+                                    err_data = os.read(self.process.stderr.fileno(), 4096).decode(
+                                        errors="replace"
+                                    )
+                                    if not err_data:
+                                        break
+                                    self.buffer.append(err_data)
+                                except (OSError, EOFError):
+                                    break
+                        except Exception:
+                            pass
 
             except Exception as e:
                 self.buffer.append(f"\n[Error reading process output: {str(e)}]\n")
@@ -369,6 +423,7 @@ def start_background_command(
         persist: bool = False,
         existing_input_buffer: Optional[InputBuffer] = None,
         use_pty: bool = False,
+        master_fd: Optional[int] = None,
     ) -> str:
         """
         Start a command in background.
@@ -390,9 +445,16 @@ def start_background_command(
             buffer = existing_buffer or CircularBuffer(max_size=max_buffer_size)
 
             # Use existing process or start new one
-            master_fd = None
-            if use_pty and HAS_PTY and platform.system() != "Windows":
-                master_fd, slave_fd = pty.openpty()
+            # Use provided master_fd (e.g., from _execute_with_timeout) or default to None
+            final_master_fd = master_fd
+
+            # Only create a new PTY if no external master_fd was provided
+            # (prevents overwriting an externally-created PTY fd)
+            can_use_pty = (
+                use_pty and master_fd is None and HAS_PTY and platform.system() != "Windows"
+            )
+            if can_use_pty:
+                final_master_fd, slave_fd = pty.openpty()
 
                 # Disable echo on the slave PTY
                 attr = termios.tcgetattr(slave_fd)
@@ -415,8 +477,13 @@ def start_background_command(
             elif existing_process:
                 process = existing_process
             else:
+                # When PTY was requested but isn't available (e.g. Windows),
+                # wrap with stdbuf -oL to force line-buffered output at the libc level
+                resolved_command = (
+                    cls._wrap_line_buffered(command) if use_pty and not HAS_PTY else command
+                )
                 process = subprocess.Popen(
-                    command,
+                    resolved_command,
                     shell=True,
                     stdout=subprocess.PIPE,
                     stderr=subprocess.PIPE,
@@ -434,7 +501,7 @@ def start_background_command(
                 buffer,
                 persist=persist,
                 input_buffer=existing_input_buffer,
-                master_fd=master_fd,
+                master_fd=final_master_fd,
             )
 
             # Generate unique key and store
@@ -519,13 +586,8 @@ def send_command_input(cls, command_key: str, text: str) -> bool:
             bg_process = cls._background_commands.get(command_key)
             if not bg_process:
                 return False
-            # Decode escape sequences (like \x1b) if present in the string
-            try:
-                text = codecs.decode(text, "unicode_escape")
-            except Exception:
-                pass
-            bg_process.send_input(text)
-            return True
+        bg_process.send_input(text)
+        return True
 
     @classmethod
     def get_all_command_outputs(cls, clear: bool = False) -> Dict[str, str]:
@@ -625,6 +687,61 @@ def list_background_commands(cls) -> Dict[str, Dict[str, any]]:
                 }
             return result
 
+    _line_buffered_tool = None
+
+    @staticmethod
+    def _detect_line_buffered_tool() -> str:
+        """
+        Detect the best available tool for forcing line-buffered stdout.
+
+        Checks for `stdbuf` (GNU coreutils, most Linux distros) and falls
+        back to `unbuffer` (expect package, available on many systems).
+        If neither is available, returns None.
+
+        Returns:
+            The tool command (e.g., 'stdbuf -oL' or 'unbuffer'), or None
+        """
+        import shutil
+
+        if shutil.which("stdbuf"):
+            return "stdbuf -oL"
+
+        if shutil.which("unbuffer"):
+            return "unbuffer"
+
+        return None
+
+    @staticmethod
+    def _wrap_line_buffered(command: str) -> str:
+        """
+        Wrap a command to force line-buffered stdout when PTY is unavailable.
+
+        When stdout is connected to a pipe instead of a TTY, most programs
+        (Python, C, Ruby, etc.) use full buffering. The stdbuf command uses
+        LD_PRELOAD to override buffering at the libc level. The unbuffer
+        command (from expect) creates a PTY wrapper.
+
+        The detected tool is cached after first check to avoid repeated
+        subprocess/shell calls.
+
+        Args:
+            command: The shell command string
+
+        Returns:
+            Command wrapped with line-buffering prefix, or the original
+            command if no tool is available
+        """
+        if BackgroundCommandManager._line_buffered_tool is None:
+            BackgroundCommandManager._line_buffered_tool = (
+                BackgroundCommandManager._detect_line_buffered_tool()
+            )
+
+        tool = BackgroundCommandManager._line_buffered_tool
+        if tool:
+            return f"{tool} {command}"
+
+        return command
+
     @staticmethod
     def save_paginated_output(
         output: str,
diff --git a/cecli/tools/command.py b/cecli/tools/command.py
index 646fd46d5ba..8fe49a4d4d6 100644
--- a/cecli/tools/command.py
+++ b/cecli/tools/command.py
@@ -3,6 +3,15 @@
 import os
 import platform
 
+# PTY support for interactive commands (avoids pipe buffering issues)
+try:
+    import pty
+    import termios
+
+    HAS_PTY = True
+except ImportError:
+    HAS_PTY = False
+
 import xxhash
 
 from cecli.helpers.background_commands import BackgroundCommandManager
@@ -21,15 +30,15 @@ class Tool(BaseTool):
         "type": "function",
         "function": {
             "name": "Command",
-            "description": "Execute a shell command.",
+            "description": "Execute a shell command or interact with background processes.",
             "parameters": {
                 "type": "object",
                 "properties": {
                     "command": {
                         "type": "string",
                         "description": (
-                            "The shell command to execute. To send stdin to an existing background"
-                            " command, use the format 'command_key::{key}'."
+                            "The shell command to execute. "
+                            "Required unless background_key is provided."
                         ),
                     },
                     "background": {
@@ -37,42 +46,44 @@ class Tool(BaseTool):
                         "description": "Run command in background (non-blocking).",
                         "default": False,
                     },
-                    "stop": {
-                        "type": "boolean",
+                    "background_key": {
+                        "type": "string",
                         "description": (
-                            "If true, stop the background command specified in the 'command'"
-                            " parameter (format 'command_key::{key}')."
+                            "Key of an existing background command to interact with. "
+                            "Use with 'action' (stdin/stop)."
                         ),
-                        "default": False,
                     },
-                    "pty": {
-                        "type": "boolean",
+                    "action": {
+                        "type": "string",
+                        "enum": ["stdin", "stop"],
                         "description": (
-                            "Run the command in a pseudo-terminal (PTY). Useful for interactive"
-                            " programs like 'vi' or 'top'."
+                            "Action on a background command. Requires background_key: "
+                            "'stdin' to send input, 'stop' to terminate."
                         ),
-                        "default": False,
                     },
                     "stdin": {
                         "type": "string",
                         "description": (
-                            "Input to send to the command's stdin. Supports escape sequences like"
-                            " \\n, \\r, \\t, and hex escapes like \\x1b."
+                            "Input to send. Use with background=True to send at "
+                            "start time, or with background_key + action='stdin'."
+                        ),
+                    },
+                    "pty": {
+                        "type": "boolean",
+                        "description": (
+                            "Use a pseudo-terminal (PTY). Auto-enabled on Unix for "
+                            "background commands. Useful for interactive programs "
+                            "like 'vi' or 'top'."
                         ),
+                        "default": False,
                     },
                 },
-                "required": ["command"],
+                "required": [],
             },
         },
     }
 
     @staticmethod
-    def _parse_command_key(command):
-        """Extract command key from command string if it follows the pattern."""
-        if command and command.startswith("command_key::"):
-            return command.split("::", 1)[1].strip()
-        return None
-
     @staticmethod
     def _hash_command(command):
         """Compute an xxhash of the full command text for session tracking."""
@@ -83,38 +94,41 @@ def _hash_command(command):
 
     @classmethod
     async def execute(
-        cls, coder, command, background=False, stop=None, stdin=None, pty=False, **kwargs
+        cls,
+        coder,
+        command=None,
+        background=False,
+        background_key=None,
+        action=None,
+        stdin=None,
+        pty=False,
+        **kwargs,
     ):
         """
-        Execute a shell command, optionally in background.
-        Commands run with timeout based on agent_config['command_timeout'] (default: 30 seconds).
-        """
-        command_key = cls._parse_command_key(command)
+        Execute a shell command or interact with background processes.
 
-        # Handle stopping background commands
-        if stop:
-            if not command_key:
-                return (
-                    "Error: 'command' in format 'command_key::{key}' is required when 'stop' is"
-                    " true."
-                )
-            return await cls._stop_background_command(coder, command_key)
+        For new commands: provide 'command' (and optionally 'background', 'stdin', 'pty').
+        For background interactions: provide 'background_key' + 'action' (stdin/stop).
 
-        # Handle sending stdin to an existing background command
-        if stdin:
-            if not command_key:
-                return (
-                    "Error: 'command' in format 'command_key::{key}' is required when using"
-                    " 'stdin'."
-                )
+        Commands run with timeout based on agent_config['command_timeout'] (default: 30 seconds).
+        """
+        # Handle interactions with an existing background command
+        if background_key:
+            if action == "stdin":
+                if not stdin:
+                    return "Error: 'stdin' is required when action='stdin'."
+                cls.clear_invocation_cache()
+                success = BackgroundCommandManager.send_command_input(background_key, stdin)
+                if success:
+                    return f"Sent input to background command {background_key}: {stdin}"
+                else:
+                    return f"Error: Background command {background_key} not found or not running."
 
-            cls.clear_invocation_cache()
+            elif action == "stop":
+                return await cls._stop_background_command(coder, background_key)
 
-            success = BackgroundCommandManager.send_command_input(command_key, stdin)
-            if success:
-                return f"Sent input to background command {command_key}: {stdin}"
             else:
-                return f"Error: Background command {command_key} not found or not running."
+                return f"Error: Unknown action '{action}'. " "Use one of: stdin, stop."
 
         if not command:
             return "Error: 'command' must be provided."
@@ -143,7 +157,7 @@ async def execute(
             timeout = coder.agent_config.get("command_timeout", 30)
 
         if background:
-            return await cls._execute_background(coder, command, use_pty=pty)
+            return await cls._execute_background(coder, command, use_pty=pty, stdin=stdin)
         elif timeout > 0:
             return await cls._execute_with_timeout(coder, command, timeout, use_pty=pty)
         else:
@@ -199,12 +213,20 @@ async def _get_confirmation(cls, coder, command_string, background):
         return confirmed
 
     @classmethod
-    async def _execute_background(cls, coder, command_string, use_pty=False):
+    async def _execute_background(cls, coder, command_string, use_pty=None, stdin=None):
         """
         Execute command in background.
+
+        Args:
+            stdin: Optional text to send to the command's stdin after starting
         """
         coder.io.tool_output(f"⛭ Starting background command: {command_string}", type="tool-result")
 
+        # Default to PTY on Unix platforms for proper line-buffered output
+        # (Python and other programs buffer output aggressively on pipes)
+        if use_pty is None:
+            use_pty = platform.system() != "Windows"
+
         # Use static manager to start background command
         command_key = BackgroundCommandManager.start_background_command(
             command_string,
@@ -214,6 +236,10 @@ async def _execute_background(cls, coder, command_string, use_pty=False):
             use_pty=use_pty,
         )
 
+        # Send stdin to the background command if provided
+        if stdin:
+            BackgroundCommandManager.send_command_input(command_key, stdin)
+
         return (
             f"Background command started: {command_string}\n"
             f"Command key: {command_key}\n"
@@ -221,13 +247,13 @@ async def _execute_background(cls, coder, command_string, use_pty=False):
         )
 
     @classmethod
-    async def _execute_with_timeout(cls, coder, command_string, timeout, use_pty=False):
+    async def _execute_with_timeout(cls, coder, command_string, timeout, use_pty=None):
         """
         Execute command with timeout. If timeout elapses, move to background.
 
-        IMPORTANT: We use a different approach to avoid pipe conflicts.
-        Instead of reading pipes directly, we let BackgroundCommandManager
-        handle all pipe reading from the start.
+        When use_pty is True (or auto-defaulted on Unix), a pseudo-terminal
+        is used to avoid the full-buffering issue that occurs when stdout is
+        connected to a pipe instead of a TTY.
         """
         import asyncio
         import subprocess
@@ -239,24 +265,59 @@ async def _execute_with_timeout(cls, coder, command_string, timeout, use_pty=Fal
             f"⛭ Executing shell command with {timeout}s timeout.", type="tool-result"
         )
 
-        shell = os.environ.get("SHELL", "/bin/sh")
+        # Auto-default to PTY on Unix unless explicitly set otherwise
+        if use_pty is None:
+            use_pty = platform.system() != "Windows"
 
         # Create output buffer
         buffer = CircularBuffer(max_size=4096)
 
-        # Start process with pipes for output capture
-        process = subprocess.Popen(
-            command_string,
-            shell=True,
-            executable=shell if platform.system() != "Windows" else None,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
-            stdin=subprocess.PIPE,
-            cwd=coder.root,
-            text=True,
-            bufsize=1,
-            universal_newlines=True,
-        )
+        # Decide whether to use PTY
+        master_fd = None
+
+        if use_pty and HAS_PTY and platform.system() != "Windows":
+            master_fd, slave_fd = pty.openpty()
+
+            # Disable echo on the slave PTY
+            attr = termios.tcgetattr(slave_fd)
+            attr[3] = attr[3] & ~termios.ECHO
+            termios.tcsetattr(slave_fd, termios.TCSANOW, attr)
+
+            process = subprocess.Popen(
+                command_string,
+                shell=True,
+                executable=os.environ.get("SHELL", "/bin/sh"),
+                stdout=slave_fd,
+                stderr=slave_fd,
+                stdin=slave_fd,
+                cwd=coder.root,
+                close_fds=True,
+                text=True,
+                bufsize=1,
+                universal_newlines=True,
+            )
+            os.close(slave_fd)
+        else:
+            # Start process with pipes for output capture
+            # When PTY was requested but unavailable, wrap with stdbuf for line-buffered output
+            resolved_cmd = (
+                BackgroundCommandManager._wrap_line_buffered(command_string)
+                if use_pty and not HAS_PTY
+                else command_string
+            )
+            shell = os.environ.get("SHELL", "/bin/sh")
+            process = subprocess.Popen(
+                resolved_cmd,
+                shell=True,
+                executable=shell if platform.system() != "Windows" else None,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+                stdin=subprocess.PIPE,
+                cwd=coder.root,
+                text=True,
+                bufsize=1,
+                universal_newlines=True,
+            )
 
         # Immediately register with background manager to handle pipe reading
         command_key = BackgroundCommandManager.start_background_command(
@@ -267,6 +328,7 @@ async def _execute_with_timeout(cls, coder, command_string, timeout, use_pty=Fal
             existing_process=process,
             existing_buffer=buffer,
             persist=True,
+            master_fd=master_fd,
         )
 
         # Now monitor the process with timeout
@@ -340,7 +402,7 @@ async def _execute_with_timeout(cls, coder, command_string, timeout, use_pty=Fal
             if elapsed >= timeout:
                 # Timeout elapsed, process continues in background
                 coder.io.tool_output(
-                    f"⏱️ Command exceeded {timeout}s timeout, continuing in background...",
+                    f"\u23f1\ufe0f Command exceeded {timeout}s timeout, continuing in background...",
                     type="tool-result",
                 )
 
@@ -428,6 +490,7 @@ async def _stop_background_command(cls, coder, command_key):
         else:
             return output  # Error message from manager
 
+    @classmethod
     async def _handle_errors(cls, coder, command_string, e):
         """Handle errors during command execution."""
         coder.io.tool_error(f"Error executing shell command: {str(e)}")
@@ -451,7 +514,8 @@ def format_output(cls, coder, mcp_server, tool_response):
 
         command = params.get("command", "")
         background = params.get("background", False)
-        stop = params.get("stop", False)
+        background_key = params.get("background_key")
+        action = params.get("action")
         stdin = params.get("stdin")
         pty = params.get("pty", False)
 
@@ -461,8 +525,8 @@ def format_output(cls, coder, mcp_server, tool_response):
         extras = []
         if background:
             extras.append("background=True")
-        if stop:
-            extras.append("stop=True")
+        if action:
+            extras.append(f"action={action}")
         if pty:
             extras.append("pty=True")
 
@@ -473,8 +537,13 @@ def format_output(cls, coder, mcp_server, tool_response):
             coder.io.tool_output(f"{color_start}Stdin:{color_end}")
             coder.io.tool_output(stdin)
 
-        coder.io.tool_output(f"{color_start}Command:{color_end}")
-        coder.io.tool_output(command)
+        if background_key and action:
+            coder.io.tool_output(f"{color_start}Background Key:{color_end} {background_key}")
+            coder.io.tool_output(f"{color_start}Action:{color_end} {action}")
+        elif command:
+            coder.io.tool_output(f"{color_start}Command:{color_end}")
+            coder.io.tool_output(command)
+
         coder.io.tool_output("")
 
         # Output footer

From a85fa60e9dfb62ce8d18fe67af416dd85eeedd41 Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Thu, 25 Jun 2026 20:20:40 -0400
Subject: [PATCH 4/9] Only give content hashes for contentful lines

---
 cecli/helpers/hashpos/hashpos.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/cecli/helpers/hashpos/hashpos.py b/cecli/helpers/hashpos/hashpos.py
index 280e3394ec4..8077e900e3d 100644
--- a/cecli/helpers/hashpos/hashpos.py
+++ b/cecli/helpers/hashpos/hashpos.py
@@ -119,7 +119,11 @@ def format_content(self, use_private_ids: bool = False, start_line: int = 1) ->
                 if use_private_ids
                 else self.generate_public_id(line, i)
             )
-            formatted_lines.append(f"{prefix}::{line}")
+            if line.strip():
+                formatted_lines.append(f"{prefix}::{line}")
+            else:
+                formatted_lines.append(f"{line}")
+
         return "\n".join(formatted_lines)
 
     def resolve_to_lines(self, public_id: str, start_line: int = 1) -> list[int]:

From 9e6e45fbe95fc1062ac799ff8a2d5a4bb991fbb4 Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Thu, 25 Jun 2026 22:59:51 -0400
Subject: [PATCH 5/9] Update py-cymbal

---
 requirements.txt                    | 2 +-
 requirements/common-constraints.txt | 2 +-
 requirements/requirements.in        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index d9800f1c66c..80fce896211 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -282,7 +282,7 @@ ptyprocess==0.7.0
     # via
     #   -c requirements/common-constraints.txt
     #   pexpect
-py-cymbal==0.1.24
+py-cymbal==0.2.1
     # via
     #   -c requirements/common-constraints.txt
     #   -r requirements/requirements.in
diff --git a/requirements/common-constraints.txt b/requirements/common-constraints.txt
index a2c112f9acc..ffc8da5939f 100644
--- a/requirements/common-constraints.txt
+++ b/requirements/common-constraints.txt
@@ -353,7 +353,7 @@ psutil==7.1.3
     #   -r requirements/requirements.in
 ptyprocess==0.7.0
     # via pexpect
-py-cymbal==0.1.24
+py-cymbal==0.2.1
     # via -r requirements/requirements.in
 pycodestyle==2.14.0
     # via flake8
diff --git a/requirements/requirements.in b/requirements/requirements.in
index 6aa96211a99..a6575c2168f 100644
--- a/requirements/requirements.in
+++ b/requirements/requirements.in
@@ -31,7 +31,7 @@ textual>=6.0.0
 tomlkit>=0.14.0
 truststore
 xxhash>=3.6.0
-py-cymbal>=0.1.24
+py-cymbal>=0.2.1
 cryptography>=42.0.0
 json-repair>=0.60.1
 

From b6a9f0c72cd99a6ec090f5af2304f4b470099e0d Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Thu, 25 Jun 2026 23:08:28 -0400
Subject: [PATCH 6/9] Let py-cymbal rock in case I push this version before the
 timeout expires

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 18525043ae3..74808f90a7a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,6 +43,7 @@ include = ["cecli*"]
 
 [tool.uv]
 exclude-newer = "2 days"
+exclude-newer-package = { "py-cymbal" = "0 days" }
 
 [build-system]
 requires = ["setuptools>=68", "setuptools_scm[toml]>=8"]

From 35c9ac01add0827f247d651556eb7883f91343d1 Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Fri, 26 Jun 2026 08:20:29 -0400
Subject: [PATCH 7/9] #587: Strip openai prefix from LLM proxies for proper
 costs and token limits

---
 cecli/models.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cecli/models.py b/cecli/models.py
index 3f593cb7b75..c06f0a1c92d 100644
--- a/cecli/models.py
+++ b/cecli/models.py
@@ -256,6 +256,8 @@ def get_model_from_cached_json_db(self, model):
 
     def get_model_info(self, model):
         cached_info = self.get_model_from_cached_json_db(model)
+        if cached_info:
+            return cached_info
         litellm_info = None
         if litellm._lazy_module or not cached_info:
             try:
@@ -268,6 +270,10 @@ def get_model_info(self, model):
             return provider_info
         if litellm_info:
             return litellm_info
+        if not cached_info and model.startswith("openai/"):
+            stripped = model[7:]
+            if stripped:
+                return self.get_model_info(stripped)
         return cached_info
 
     def _resolve_via_provider(self, model, cached_info):

From 931c220b18662e233c291ed2453a327102af373b Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Fri, 26 Jun 2026 08:41:24 -0400
Subject: [PATCH 8/9] Fix cache hit token cost calculator

---
 cecli/coders/base_coder.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/cecli/coders/base_coder.py b/cecli/coders/base_coder.py
index bb677a15e68..119fc80fe43 100755
--- a/cecli/coders/base_coder.py
+++ b/cecli/coders/base_coder.py
@@ -4023,7 +4023,9 @@ def compute_costs_from_tokens(
         input_cost_per_token = self.get_active_model().info.get("input_cost_per_token") or 0
         output_cost_per_token = self.get_active_model().info.get("output_cost_per_token") or 0
         input_cost_per_token_cache_hit = (
-            self.get_active_model().info.get("input_cost_per_token_cache_hit") or 0
+            self.get_active_model().info.get("input_cost_per_token_cache_hit")
+            or self.get_active_model().info.get("cache_read_input_token_cost")
+            or 0
         )
 
         # deepseek
@@ -4035,14 +4037,13 @@ def compute_costs_from_tokens(
         #    == total tokens that were
 
         if input_cost_per_token_cache_hit:
-            # must be deepseek
-            cost += input_cost_per_token_cache_hit * cache_hit_tokens
-            cost += (prompt_tokens - input_cost_per_token_cache_hit) * input_cost_per_token
+            cost += cache_hit_tokens * input_cost_per_token_cache_hit
+            cost += (prompt_tokens - cache_hit_tokens) * input_cost_per_token
         else:
             # hard code the anthropic adjustments, no-ops for other models since cache_x_tokens==0
             cost += cache_write_tokens * input_cost_per_token * 1.25
             cost += cache_hit_tokens * input_cost_per_token * 0.10
-            cost += prompt_tokens * input_cost_per_token
+            cost += (prompt_tokens - cache_hit_tokens) * input_cost_per_token
 
         cost += completion_tokens * output_cost_per_token
         return cost

From adb7218205b397bd0664aa57eab4f9e427eb89d6 Mon Sep 17 00:00:00 2001
From: Your Name <you@example.com>
Date: Fri, 26 Jun 2026 08:52:39 -0400
Subject: [PATCH 9/9] #584: Remove ambient refresh interval from non-TUI mode

---
 cecli/io.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cecli/io.py b/cecli/io.py
index 4a703eaa22f..a140bd516a9 100644
--- a/cecli/io.py
+++ b/cecli/io.py
@@ -514,7 +514,6 @@ def __init__(
                 "lexer": PygmentsLexer(MarkdownLexer),
                 "editing_mode": self.editingmode,
                 "bottom_toolbar": self.get_bottom_toolbar,
-                "refresh_interval": 0.1,
             }
             if self.editingmode == EditingMode.VI:
                 session_kwargs["cursor"] = ModalCursorShapeConfig()