PyModel
diff --git a/‎.gitignore‎
Lines changed: 1 addition & 0 deletions b/‎.gitignore‎
Lines changed: 1 addition & 0 deletions
diff --git a/‎CHANGELOG.md‎
Lines changed: 6 additions & 0 deletions b/‎CHANGELOG.md‎
Lines changed: 6 additions & 0 deletions
diff --git a/‎packages/pythinker-core/tests/test_anthropic_thinking.py‎
Lines changed: 12 additions & 0 deletions b/‎packages/pythinker-core/tests/test_anthropic_thinking.py‎
Lines changed: 12 additions & 0 deletions
diff --git a/‎packages/pythinker-host/src/pythinker_host/__init__.py‎
Lines changed: 8 additions & 0 deletions b/‎packages/pythinker-host/src/pythinker_host/__init__.py‎
Lines changed: 8 additions & 0 deletions
diff --git a/‎packages/pythinker-host/src/pythinker_host/local.py‎
Lines changed: 8 additions & 2 deletions b/‎packages/pythinker-host/src/pythinker_host/local.py‎
Lines changed: 8 additions & 2 deletions
diff --git a/‎packages/pythinker-host/src/pythinker_host/path.py‎
Lines changed: 4 additions & 0 deletions b/‎packages/pythinker-host/src/pythinker_host/path.py‎
Lines changed: 4 additions & 0 deletions
diff --git a/‎packages/pythinker-host/src/pythinker_host/ssh.py‎
Lines changed: 23 additions & 0 deletions b/‎packages/pythinker-host/src/pythinker_host/ssh.py‎
Lines changed: 23 additions & 0 deletions
diff --git a/‎packages/pythinker-review/tests/unit/test_security_intel.py‎
Lines changed: 2 additions & 1 deletion b/‎packages/pythinker-review/tests/unit/test_security_intel.py‎
Lines changed: 2 additions & 1 deletion
diff --git a/‎src/pythinker_code/__main__.py‎
Lines changed: 0 additions & 58 deletions b/‎src/pythinker_code/__main__.py‎
Lines changed: 0 additions & 58 deletions
diff --git a/‎src/pythinker_code/acp/host.py‎
Lines changed: 3 additions & 0 deletions b/‎src/pythinker_code/acp/host.py‎
Lines changed: 3 additions & 0 deletions
@@ -77,3 +77,4 @@ blackbox/
 .coverage.*
 coverage.xml
 htmlcov/
+*.scratchpad.lock
@@ -15,6 +15,12 @@ GitHub Releases page; `0.8.0` is the new starting line.
 
 ## Unreleased
 
+- **Deep-audit remediation: security, correctness, and multi-instance robustness.** Permission gate: awk programs that shell out via `print | "cmd"` / `getline` are now classified as mutating AND destructive (previously only `system(`/`>` and only mutating), and `xargs -L N` no longer hides its payload from classification. Glob resolves symlinks before its workspace-boundary check (an in-workspace symlink could previously list outside content); progress-note titles are ANSI-sanitized like every other transcript field. Grep content lines are parsed with unambiguous field separators, so paths like `utf-8-codec.py` are no longer mangled with `-n=false` and sensitive-file attribution is exact. Multi-line edits on CRLF files work again (LF-joined old strings are CRLF-translated when needed). `/import` preserves paths byte-for-byte (only a standalone leading/trailing `--force` is treated as the flag). Post-compaction file reminders include `--add-dir` files. Double-interrupt can no longer orphan the interruption-marker write (unanswered tool_calls). Background web replay falls back to full history (not empty) when the watermark stat fails, and a malformed Agent resume id returns a clean "Agent not found". OAuth: login fails loud when the token response lacks a `refresh_token`; a refresh response without `expires_in` carries the previous lifetime forward instead of refreshing every tick; the device-id file can no longer be read empty mid-creation. A failed `theme="auto"` background probe can be retried by re-selecting auto via `/theme`. Multi-instance: sessions now take a per-session writer lock (a second `pythinker -r <id>`/web worker on the same session is refused instead of interleaving turns), the shared `pythinker.json` index uses a locked read-modify-write (no more lost work-dir registrations), JSONL appenders repair torn final lines after a crash, forks materialize atomically, project-memory mutations abort on read failure instead of wiping the file, the journal is capped at 100 recaps, inbox approve/reject claims candidates atomically, and recall re-arms when another instance writes new memory. Subagents: a failed summary continuation no longer discards a completed agent's work, hallucinated subagent types fail fast with the valid-type list (before any RunAgents child launches), background failures carry an `Agent ID:` + resume hint, and a crash inside the runner's own error handling is logged instead of silently lost.
+- **Breaking (CLI flags): `pythinker web` / `pythinker vis` host short flag is now `-H`.** `-h` is a help alias on both subcommands (matching the root CLI); previously `-h <ip>` bound the host. Scripts using `-h 0.0.0.0` now print help and exit 0 without starting a server — switch to `-H <ip>` or `--host <ip>`. Part of the security/correctness audit (which also confined Grep to the workspace, gated non-HTTPS provider URLs in the web config API to loopback, and stopped saving OpenAI keys on 401/403).
+- **Thinking effort moved to a single top-right label on the input border.** The input box border is now one static frame grey at every effort level instead of recoloring the whole bar cold→hot, and the effort is no longer duplicated in the footer line. It's shown once, as a small label flushed to the right of the input's top border — a level-colored dot (slate→blue→teal→amber→orange→red as `off→max`) plus the muted level word — so the dial stays glanceable without tinting the typing area or cluttering the footer. The label is hidden entirely for native-thinking models (`always_thinking`, no user dial) and non-thinking models, and the rule auto-shortens by the label width so the line never wraps.
+- **Qwen models treated as native-thinking across both plans.** Qwen3.x/3.7 (e.g. `qwen3.7-max`, `qwen3.6-plus`, the Qwen3 Coder models) now carry the `always_thinking` capability on both the Alibaba Model Studio and OpenCode Go plans, matching GLM/MiniMax: reasoning is built in and always on, with no user effort dial and no top-border effort label. Reasoning still flows over the Anthropic `thinking` block that both Anthropic-compatible routes accept.
+- **TUI enhancements: adaptive theme, layout, and agent prompt overhaul.** Adaptive terminal-background probe + color-depth blending; reference-CLI layout and palette refinements; unified todo-list renderer; white running-task titles with consistent diff palette; elapsed/tokens/t-s metadata on the background status line; transcript-row bullet fix; renderer guards and markdown fence table unwrapping. All default agent prompts restructured with explicit Mission / Hard Constraints / Workflow / Output Contract sections. Background manager and subagent runner hardened with stale-record reconciliation and resume contract enforcement. Automatic turn recaps disabled by default.
+
 ## 0.39.0 (2026-06-09)
 
 - **Refreshed TUI theme and Catppuccin syntax highlighting.** The interface adopts a brand periwinkle/indigo accent (`#B3B9F4` dark / `#0B114E` light) with a reharmonized selection tint, and code blocks now highlight with Catppuccin Mocha (dark) / Latte (light), adaptive to the active theme — implemented as foreground-only Pygments styles with no new dependency. Markdown inline code and links render terminal-native cyan, blockquotes green, and ordered-list markers bright blue (so they adapt per terminal), and user messages sit on a neutral grey block instead of the prior blue tint.
 
@@ -114,6 +114,18 @@ def test_supports_adaptive_thinking(model: str, expected: bool) -> None:
         ("claude-opus-4-8", "max", "max"),
         ("claude-opus-5-0", "max", "max"),
         ("claude-opus-5-0", "xhigh", "high"),
+        # Qwen via the Anthropic-compatible endpoint (Alibaba Model Studio /
+        # OpenCode Go @ai-sdk/anthropic): a non-Claude model, so it takes the
+        # pre-4.6 budget path. Effort must land in {low, medium, high} so the
+        # budgets[...] lookup in with_thinking can never KeyError, and xhigh/max
+        # clamp to high while minimal floors to low.
+        ("qwen3.7-max", "off", "off"),
+        ("qwen3.7-max", "minimal", "low"),
+        ("qwen3.7-max", "low", "low"),
+        ("qwen3.7-max", "medium", "medium"),
+        ("qwen3.7-max", "high", "high"),
+        ("qwen3.7-max", "xhigh", "high"),
+        ("qwen3.7-max", "max", "high"),
     ],
 )
 def test_clamp_effort(model: str, effort: str, expected: str) -> None:
 
@@ -156,6 +156,10 @@ async def chdir(self, path: StrOrHostPath) -> None:
         """Change the current working directory."""
         ...
 
+    async def realpath(self, path: StrOrHostPath) -> HostPath:
+        """Resolve symlinks and return the real absolute path."""
+        ...
+
     async def stat(self, path: StrOrHostPath, *, follow_symlinks: bool = True) -> StatResult:
         """Get the stat result for a path."""
         ...
@@ -282,6 +286,10 @@ async def chdir(path: StrOrHostPath) -> None:
     await get_current_host().chdir(path)
 
 
+async def realpath(path: StrOrHostPath) -> HostPath:
+    return await get_current_host().realpath(path)
+
+
 async def stat(path: StrOrHostPath, *, follow_symlinks: bool = True) -> StatResult:
     return await get_current_host().stat(path, follow_symlinks=follow_symlinks)
 
 
@@ -99,6 +99,12 @@ async def chdir(self, path: StrOrHostPath) -> None:
         local_path = path.unsafe_to_local_path() if isinstance(path, HostPath) else Path(path)
         os.chdir(local_path)
 
+    async def realpath(self, path: StrOrHostPath) -> HostPath:
+        """Resolve symlinks and return the real path (follows symlinks)."""
+        local = path.unsafe_to_local_path() if isinstance(path, HostPath) else Path(path)
+        resolved = await asyncio.to_thread(os.path.realpath, str(local))
+        return HostPath.unsafe_from_local_path(Path(resolved))
+
     async def stat(self, path: StrOrHostPath, *, follow_symlinks: bool = True) -> StatResult:
         local_path = path.unsafe_to_local_path() if isinstance(path, HostPath) else Path(path)
         st = await aiofiles.os.stat(local_path, follow_symlinks=follow_symlinks)
@@ -143,7 +149,7 @@ async def readtext(
         errors: Literal["strict", "ignore", "replace"] = "strict",
     ) -> str:
         local_path = path.unsafe_to_local_path() if isinstance(path, HostPath) else Path(path)
-        async with aiofiles.open(local_path, encoding=encoding, errors=errors) as f:
+        async with aiofiles.open(local_path, encoding=encoding, errors=errors, newline="") as f:
             return await f.read()
 
     async def readlines(
@@ -154,7 +160,7 @@ async def readlines(
         errors: Literal["strict", "ignore", "replace"] = "strict",
     ) -> AsyncGenerator[str]:
         local_path = path.unsafe_to_local_path() if isinstance(path, HostPath) else Path(path)
-        async with aiofiles.open(local_path, encoding=encoding, errors=errors) as f:
+        async with aiofiles.open(local_path, encoding=encoding, errors=errors, newline="") as f:
             async for line in f:
                 yield line
 
 
@@ -118,6 +118,10 @@ def expanduser(self) -> HostPath:
             return home
         return home.joinpath(*parts[1:])
 
+    async def realpath(self) -> HostPath:
+        """Resolve symlinks and return the real absolute path."""
+        return await pythinker_host.realpath(self)
+
     async def stat(self, follow_symlinks: bool = True) -> pythinker_host.StatResult:
         """Return an os.stat_result for the path."""
         return await pythinker_host.stat(self, follow_symlinks=follow_symlinks)
 
@@ -179,6 +179,29 @@ async def chdir(self, path: StrOrHostPath) -> None:
         await self._sftp.chdir(str(path))
         self._cwd = await self._sftp.realpath(".")
 
+    async def realpath(self, path: StrOrHostPath) -> HostPath:
+        """Resolve symlinks and return the real path via SFTP realpath.
+
+        ``os.path.realpath`` tolerates a missing leaf (resolves the existing
+        parent and re-appends the rest); strict SFTP servers instead error on
+        nonexistent paths, which would break e.g. WriteFile creating a new
+        file. Mirror the local tolerance by resolving the deepest existing
+        ancestor and re-appending the missing suffix.
+        """
+        parts: list[str] = []
+        candidate = posixpath.normpath(str(path))
+        while True:
+            try:
+                real = await self._sftp.realpath(candidate)
+            except asyncssh.SFTPError:
+                parent = posixpath.dirname(candidate)
+                if parent == candidate:  # filesystem root failed: give up
+                    raise OSError(f"realpath failed for {path}") from None
+                parts.append(posixpath.basename(candidate))
+                candidate = parent
+                continue
+            return HostPath(posixpath.join(real, *reversed(parts)) if parts else real)
+
     async def stat(
         self,
         path: StrOrHostPath,
 
@@ -48,7 +48,8 @@ def test_intel_client_disables_implicit_redirects() -> None:
     from pythinker_review.security_intel.client import IntelHttpClient
 
     client = IntelHttpClient()
-    assert any(isinstance(h, _NoRedirectHandler) for h in client._opener.handlers)
+    handlers = client._opener.handlers  # pyright: ignore[reportAttributeAccessIssue]
+    assert any(isinstance(h, _NoRedirectHandler) for h in handlers)
 
 
 def test_intel_cache_roundtrip(tmp_path: Path) -> None:
 
@@ -8,60 +8,6 @@
 if TYPE_CHECKING:
     from typing import TextIO
 
-ROOT_HELP = """Usage: pythinker [OPTIONS] COMMAND [ARGS]...
-
-  Pythinker, your next CLI agent.
-
-Options:
-  -h, --help                       Show this message and exit.
-  -V, --version                    Show version and exit.
-  --verbose                        Print verbose information.
-  --debug                          Log debug information.
-  -w, --work-dir DIRECTORY         Working directory for the agent.
-  --add-dir DIRECTORY              Add an additional workspace directory.
-  -S, -r, --session, --resume TEXT Resume a session.
-  -C, --continue                   Continue the previous session.
-  --config TEXT                    Config TOML/JSON string to load.
-  --config-file FILE               Config TOML/JSON file to load.
-  -m, --model TEXT                 LLM model to use.
-  --thinking / --no-thinking       Enable or disable thinking mode.
-  -y, --yolo, --yes, --auto-approve
-                                   Dangerously skip permission approvals.
-  --plan                           Start in plan mode.
-  --auto                           Run in auto mode (no user present).
-  -p, -c, --prompt, --command TEXT User prompt to the agent.
-  --print                          Run in print mode.
-  --acp                            Deprecated; use `pythinker acp`.
-  --wire                           Run as Wire server.
-  --quiet                          Print only the final assistant message.
-  --agent [default|okabe]          Builtin agent specification to use.
-  --agent-file FILE                Custom agent specification file.
-  --mcp-config-file FILE           MCP config file to load; repeatable.
-  --mcp-config TEXT                MCP config JSON to load; repeatable.
-  --skills-dir DIRECTORY           Custom skills directory; repeatable.
-  --no-telemetry                   Disable anonymous telemetry & error reporting.
-
-Commands:
-  acp      Run Pythinker CLI ACP server.
-  term     Run Toad TUI backed by Pythinker CLI ACP server.
-  login    Login with a model provider.
-  logout   Logout from a model provider.
-  info     Show version and protocol information.
-  export   Export session data.
-  mcp      Manage MCP server configurations.
-  plugin   Manage plugins.
-  review          Diff-focused code review (delegates to pythinker-review).
-  secscan         Diff-focused security review (delegates to pythinker-review).
-  security-scan   Repo-wide Pythinker Security Scan pipeline (Python-native).
-  debug           Failure/log root-cause analysis (delegates to pythinker-review).
-  update   Check for and install Pythinker CLI updates.
-  vis      Run Pythinker Agent Tracing Visualizer.
-  web      Run Pythinker CLI web interface.
-
-Documentation:        https://pythoughts-labs.github.io/pythinker-code/
-LLM friendly version: https://pythoughts-labs.github.io/pythinker-code/llms.txt
-"""
-
 
 def _prog_name() -> str:
     return Path(sys.argv[0]).name or "pythinker"
@@ -126,10 +72,6 @@ def main(argv: Sequence[str] | None = None) -> int | str | None:
         print(f"pythinker, version {get_version()} — by {ORGANIZATION}")
         return 0
 
-    if len(args) == 1 and args[0] in {"--help", "-h"}:
-        print(ROOT_HELP, end="")
-        return 0
-
     from pythinker_code.telemetry.crash import install_crash_handlers, set_phase
     from pythinker_code.utils.proxy import normalize_proxy_env
 
 
@@ -212,6 +212,9 @@ def getcwd(self) -> HostPath:
     async def chdir(self, path: StrOrHostPath) -> None:
         await self._fallback.chdir(path)
 
+    async def realpath(self, path: StrOrHostPath) -> HostPath:
+        return await self._fallback.realpath(path)
+
     async def stat(self, path: StrOrHostPath, *, follow_symlinks: bool = True) -> StatResult:
         return await self._fallback.stat(path, follow_symlinks=follow_symlinks)