fix: pin app compose commands so an app op can never take down the core stack

.serena/.gitignore

@@ -0,0 +1,2 @@
+/cache
+/project.local.yml

.serena/project.yml

@@ -0,0 +1,159 @@
+# the name by which the project can be referenced within Serena/when chatting with the LLM.
+project_name: "issue-160"
+
+# list of languages for which language servers are started (LSP backend only); choose from:
+#   ada                 al                  angular             ansible             bash
+#   bsl                 clojure             cpp                 cpp_ccls            crystal
+#   csharp              csharp_omnisharp    cue                 dart                elixir
+#   elm                 erlang              fortran             fsharp              gdscript
+#   go                  groovy              haskell             haxe                hlsl
+#   html                java                json                julia               kotlin
+#   latex               lean4               lua                 luau                markdown
+#   matlab              msl                 nix                 ocaml               pascal
+#   perl                php                 php_phpactor        php_phpantom        powershell
+#   python              python_jedi         python_pyrefly      python_ty           r
+#   rego                ruby                ruby_solargraph     rust                scala
+#   scss                solidity            svelte              swift               systemverilog
+#   terraform           toml                typescript          typescript_vts      vue
+#   yaml                zig
+#   (This list may be outdated; generated with scripts/print_language_list.py;
+#   For the current list, see values of Language enum here:
+#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
+# For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
+# Note:
+#   - For C, use cpp
+#   - For JavaScript, use typescript
+#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
+#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
+#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
+#   - For Free Pascal/Lazarus, use pascal
+# Special requirements:
+#   Some languages require additional setup/installations.
+#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
+# When using multiple languages, the first language server that supports a given file will be used for that file.
+# The first language is the default language and the respective language server will be used as a fallback.
+# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
+languages:
+- python
+
+# the encoding used by text files in the project
+# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
+encoding: "utf-8"
+
+# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
+# the command runs in the project root directory and is only executed if the project is trusted
+# (see trusted_project_path_patterns in the global configuration).
+# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
+# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
+# backstop for non-terminating commands; on expiry the process is killed and activation continues.
+# example: activation_command: "npx nx run-many -t build"
+activation_command:
+
+# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
+# must be a positive number.
+activation_command_timeout: 180
+
+# line ending convention to use when writing source files.
+# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
+# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
+line_ending:
+
+# The language backend to use for this project.
+# If not set, the global setting from serena_config.yml is used.
+# Valid values: LSP, JetBrains
+# Note: the backend is fixed at startup. If a project with a different backend
+# is activated post-init, an error will be returned.
+language_backend:
+
+# whether to use project's .gitignore files to ignore files
+ignore_all_files_in_gitignore: true
+
+# advanced configuration option allowing to configure language server-specific options.
+# Maps the language key to the options.
+# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
+ls_specific_settings: {}
+
+# list of workspace folder paths (LSP backend only).
+# These folders will be used to build up Serena's symbol index.
+# Paths must be within the project root and should thus be relative to the project root.
+# Furthermore, the paths should not be filtered by ignore settings.
+# Default setting: The entire project root folder (".") is considered.
+# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
+#   ls_workspace_folders:
+#     - "./subproject1"
+#     - "./subproject2"
+ls_workspace_folders: ["."]
+
+# list of additional workspace folder paths for cross-package reference support.
+# Paths can be absolute or relative to the project root.
+# Each folder is registered as an LSP workspace folder, enabling language servers to discover
+# symbols and references across package boundaries, but these folders are not indexed by Serena,
+# i.e. the respective symbols will not be found using Serena's symbol search tools.
+# Example:
+#   additional_workspace_folders:
+#     - ../sibling-package
+#     - ../shared-lib
+ls_additional_workspace_folders: []
+
+# list of additional paths to ignore in this project.
+# Same syntax as gitignore, so you can use * and **.
+# Note: global ignored_paths from serena_config.yml are also applied additively.
+ignored_paths: []
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+# list of tool names to exclude.
+# This extends the existing exclusions (e.g. from the global configuration)
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+excluded_tools: []
+
+# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
+# This extends the existing inclusions (e.g. from the global configuration).
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+included_optional_tools: []
+
+# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
+# This cannot be combined with non-empty excluded_tools or included_optional_tools.
+# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+fixed_tools: []
+
+# list of mode names that are to be activated by default, overriding the setting in the global configuration.
+# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
+# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
+# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
+# for this project.
+# This setting can, in turn, be overridden by CLI parameters (--mode).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
+default_modes:
+
+# list of mode names to be activated additionally for this project, e.g. ["query-projects"]
+# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
+added_modes:
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ""
+
+# time budget (seconds) per tool call for the retrieval of additional symbol information
+# such as docstrings or parameter information.
+# This overrides the corresponding setting in the global configuration; see the documentation there.
+# If null or missing, use the setting from the global configuration.
+symbol_info_budget:
+
+# list of regex patterns which, when matched, mark a memory entry as read‑only.
+# Extends the list from the global configuration, merging the two lists.
+read_only_memory_patterns: []
+
+# list of regex patterns for memories to completely ignore.
+# Matching memories will not appear in list_memories or activate_project output
+# and cannot be accessed via read_memory or write_memory.
+# To access ignored memory files, use the read_file tool on the raw file path.
+# Extends the list from the global configuration, merging the two lists.
+# Example: ["_archive/.*", "_episodes/.*"]
+ignored_memory_patterns: []

agents.md

@@ -48,6 +48,9 @@ shard_core/
   util/               → Shared utilities
     async_util.py       BackgroundTask, PeriodicTask, CronTask
     signals.py          Blinker signal definitions
+    subprocess.py       Async subprocess runner; app_compose_command() pins every app
+                        compose call to <app_dir>/docker-compose.yml and project <app>
+                        — never rely on cwd, compose walks up to the core stack
 ```
 
 ## Commands

shard_core/service/app_tools.py

@@ -17,16 +17,18 @@
 from shard_core.settings import settings
 from shard_core.util import signals
 from shard_core.util.misc import throttle
-from shard_core.util.subprocess import subprocess, SubprocessError, compose_command
+from shard_core.util.subprocess import subprocess, SubprocessError, app_compose_command
 
 log = logging.getLogger(__name__)
 
 
+def _app_compose(name: str) -> tuple[str, ...]:
+    return app_compose_command(get_installed_apps_path() / name)
+
+
 async def docker_create_app_containers(name: str):
     log.debug(f"creating containers for app {name}")
-    await subprocess(
-        *compose_command(), "up", "--no-start", cwd=get_installed_apps_path() / name
-    )
+    await subprocess(*_app_compose(name), "up", "--no-start")
 
 
 @throttle(5)
@@ -43,30 +45,20 @@ async def docker_start_app(name: str):
     if app_status in [Status.STOPPED, Status.RUNNING, Status.DOWN]:
         log.debug(f"starting app {name=}")
         try:
-            await subprocess(
-                *compose_command(), "up", "-d", cwd=get_installed_apps_path() / name
-            )
+            await subprocess(*_app_compose(name), "up", "-d")
         except SubprocessError as e:
             if "network" in str(e) and "not found" in str(e):
                 log.warning(
                     f"stale network reference for app {name=}, recreating containers"
                 )
-                await subprocess(
-                    *compose_command(), "down", cwd=get_installed_apps_path() / name
-                )
-                await subprocess(
-                    *compose_command(), "up", "-d", cwd=get_installed_apps_path() / name
-                )
+                await subprocess(*_app_compose(name), "down")
+                await subprocess(*_app_compose(name), "up", "-d")
             elif "Conflict" in str(e) and "already in use" in str(e):
                 log.warning(
                     f"stale containers for app {name=}, removing and recreating"
                 )
-                await subprocess(
-                    *compose_command(), "down", cwd=get_installed_apps_path() / name
-                )
-                await subprocess(
-                    *compose_command(), "up", "-d", cwd=get_installed_apps_path() / name
-                )
+                await subprocess(*_app_compose(name), "down")
+                await subprocess(*_app_compose(name), "up", "-d")
             else:
                 raise
         async with db_conn() as conn:
@@ -84,9 +76,7 @@ async def docker_pause_app(name: str):
     if app_status == Status.RUNNING:
         log.debug(f"pausing app {name=}")
         pause_started = time.monotonic()
-        await subprocess(
-            *compose_command(), "pause", cwd=get_installed_apps_path() / name
-        )
+        await subprocess(*_app_compose(name), "pause")
         await memory_pressure.reclaim_compose_stack(name)
         pause_metrics.record_pause_latency((time.monotonic() - pause_started) * 1000)
         pause_metrics.record_app_transition(name, Status.RUNNING, Status.PAUSED)
@@ -104,9 +94,7 @@ async def docker_unpause_app(name: str):
     if app_status == Status.PAUSED:
         log.debug(f"unpausing app {name=}")
         unpause_started = time.monotonic()
-        await subprocess(
-            *compose_command(), "unpause", cwd=get_installed_apps_path() / name
-        )
+        await subprocess(*_app_compose(name), "unpause")
         pause_metrics.record_unpause_latency(
             (time.monotonic() - unpause_started) * 1000
         )
@@ -125,12 +113,8 @@ async def docker_stop_app(name: str, set_status: bool = True):
     if app_status in [Status.RUNNING, Status.PAUSED, Status.UNINSTALLING]:
         if app_status == Status.PAUSED:
             # a frozen container cannot be stopped — unfreeze first
-            await subprocess(
-                *compose_command(), "unpause", cwd=get_installed_apps_path() / name
-            )
-        await subprocess(
-            *compose_command(), "stop", cwd=get_installed_apps_path() / name
-        )
+            await subprocess(*_app_compose(name), "unpause")
+        await subprocess(*_app_compose(name), "stop")
         if set_status:
             pause_metrics.record_app_transition(
                 name, Status(app_status), Status.STOPPED
@@ -150,12 +134,8 @@ async def docker_shutdown_app(name: str, set_status: bool = True, force: bool =
         if app_status == Status.PAUSED:
             # only reachable with force=True (process shutdown) — unfreeze so
             # compose down can stop and remove the containers
-            await subprocess(
-                *compose_command(), "unpause", cwd=get_installed_apps_path() / name
-            )
-        await subprocess(
-            *compose_command(), "down", cwd=get_installed_apps_path() / name
-        )
+            await subprocess(*_app_compose(name), "unpause")
+        await subprocess(*_app_compose(name), "down")
         if set_status:
             async with db_conn() as conn:
                 await db_installed_apps.update_status(conn, name, Status.DOWN)

shard_core/service/memory_pressure.py

@@ -5,7 +5,7 @@
 from pathlib import Path
 
 from shard_core.settings import settings
-from shard_core.util.subprocess import subprocess, compose_command
+from shard_core.util.subprocess import subprocess, app_compose_command
 
 log = logging.getLogger(__name__)
 
@@ -32,7 +32,7 @@ async def reclaim_compose_stack(app_name: str):
     """Write each container's current RSS to its cgroup memory.reclaim,
     proactively paging the frozen processes' anonymous pages out to swap."""
     app_path = Path(settings().path_root) / "core" / "installed_apps" / app_name
-    stdout = await subprocess(*compose_command(), "ps", "-q", cwd=app_path)
+    stdout = await subprocess(*app_compose_command(app_path), "ps", "-q")
     container_ids = [line.strip() for line in stdout.splitlines() if line.strip()]
     for container_id in container_ids:
         # The memory.reclaim write blocks while the kernel pages out — run it

shard_core/util/subprocess.py

@@ -1,10 +1,19 @@
 import asyncio
 import functools
 import logging
+import re
 import subprocess as _sp
+from pathlib import Path
 
 log = logging.getLogger(__name__)
 
+COMPOSE_FILE_NAME = "docker-compose.yml"
+
+# The core stack's compose project — an app command must never resolve to it.
+CORE_PROJECT_NAME = "core"
+
+_PROJECT_NAME_INVALID_CHARS_RE = re.compile(r"[^a-z0-9_-]")
+
 
 @functools.lru_cache(maxsize=1)
 def _detect_compose_command() -> tuple[str, ...]:
@@ -25,6 +34,40 @@ def compose_command() -> tuple[str, ...]:
     return _detect_compose_command()
 
 
+def normalize_project_name(name: str) -> str:
+    """Mirror compose's own directory-name -> project-name normalization:
+    lowercase, drop everything outside [a-z0-9_-], strip leading _ and -."""
+    return _PROJECT_NAME_INVALID_CHARS_RE.sub("", name.lower()).lstrip("_-")
+
+
+def app_compose_command(app_dir: Path) -> tuple[str, ...]:
+    """Build a compose command pinned to one app's compose file and project.
+
+    Without -f/-p, compose derives both from the working directory and walks up
+    the tree when no compose file is there — from an app dir that lands on the
+    core stack, so an app `stop`/`down` takes the whole shard offline.
+    """
+    compose_file = app_dir / COMPOSE_FILE_NAME
+    if not compose_file.is_file():
+        raise ComposeFileNotFound(compose_file)
+    project_name = normalize_project_name(app_dir.name)
+    if not project_name:
+        raise ComposeProjectNotAllowed(f"app dir {app_dir} has no valid project name")
+    if project_name == CORE_PROJECT_NAME:
+        raise ComposeProjectNotAllowed(
+            f"app dir {app_dir} resolves to the core compose project"
+        )
+    return (
+        *compose_command(),
+        "-f",
+        str(compose_file),
+        "-p",
+        project_name,
+        "--project-directory",
+        str(app_dir),
+    )
+
+
 async def subprocess(*args, cwd=None):
     process = await asyncio.create_subprocess_exec(
         *args, cwd=cwd, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE
@@ -50,3 +93,11 @@ async def subprocess(*args, cwd=None):
 
 class SubprocessError(Exception):
     pass
+
+
+class ComposeFileNotFound(Exception):
+    pass
+
+
+class ComposeProjectNotAllowed(Exception):
+    pass