@smilintux/skcapstone 0.10.0 → 0.12.5

package/src/skcapstone/cli/upgrade_cmd.py

@@ -11,6 +11,7 @@ Commands:
 
 from __future__ import annotations
 
+import logging
 import subprocess
 import sys
 from pathlib import Path
@@ -18,22 +19,27 @@ from typing import Optional
 
 import click
 
+logger = logging.getLogger(__name__)
+
 from ._common import AGENT_HOME, console
 
 # ── Package definitions ───────────────────────────────────────────────────────
 
 # Core packages: always upgraded when installed; always offered for install.
 CORE_PACKAGES: list[str] = [
-    "skmemory",    # persistent memory layer
-    "capauth",     # sovereign identity + PGP auth
-    "skcapstone",  # main agent framework
+    "capauth",          # sovereign identity + PGP auth
+    "cloud9",  # emotional continuity (FEB, OOF, Cloud 9)
+    "skmemory",         # persistent memory layer
+    "skcapstone",       # main agent framework
 ]
 
 # Optional pillar packages: upgraded only when already installed.
 # If NOT installed, the user is prompted whether they want to add them.
 OPTIONAL_PACKAGES: list[str] = [
-    "skcomm",   # P2P transport layer
-    "skchat",   # agent messaging daemon
+    "skcomms",     # P2P transport layer
+    "skchat",     # agent messaging daemon
+    "sksecurity", # security audit + threat intelligence
+    "skseed",     # seed framework for consciousness
 ]
 
 # All sovereign packages in dependency order
@@ -62,8 +68,8 @@ def _get_installed_version(package: str) -> Optional[str]:
         for line in result.stdout.splitlines():
             if line.startswith("Version:"):
                 return line.split(":", 1)[1].strip()
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.debug("Failed to get installed version for %s: %s", package, exc)
     return None
 
 
@@ -91,8 +97,8 @@ def _get_latest_version(package: str) -> Optional[str]:
                     versions = [v.strip() for v in parts[-1].split(",")]
                     if versions:
                         return versions[0]
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.debug("Failed to get latest PyPI version for %s: %s", package, exc)
     return None
 
 
@@ -161,11 +167,14 @@ def _restart_daemon(home: Path) -> None:
 # ── Package descriptions ──────────────────────────────────────────────────────
 
 _PKG_DESCRIPTIONS: dict[str, str] = {
-    "skmemory": "persistent memory layer (required by skcapstone)",
     "capauth": "sovereign PGP identity + authentication",
+    "cloud9": "emotional continuity protocol (FEB, OOF, Cloud 9)",
+    "skmemory": "persistent memory layer (required by skcapstone)",
     "skcapstone": "main sovereign agent framework",
-    "skcomm": "P2P transport layer for agent messaging",
+    "skcomms": "P2P transport layer for agent messaging",
     "skchat": "agent messaging daemon + MCP server",
+    "sksecurity": "security audit + threat intelligence",
+    "skseed": "seed framework for consciousness calibration",
 }
 
 
@@ -388,7 +397,7 @@ def register_upgrade_commands(main: click.Group) -> None:
         Upgrades all currently installed sovereign packages (skcapstone,
         skmemory, capauth) and any optional pillars already present.
 
-        For optional packages that are NOT installed (skcomm, skchat),
+        For optional packages that are NOT installed (skcomms, skchat),
         you will be prompted whether you want to add them — unless
         --yes (skip) or --all (install all) is passed.
 
@@ -402,7 +411,7 @@ def register_upgrade_commands(main: click.Group) -> None:
           skcapstone upgrade --all                 # upgrade + install all pillars
           skcapstone upgrade --force-reinstall     # overwrite ALL components
           skcapstone upgrade --force-reinstall --all  # reinstall everything
-          skcapstone upgrade --packages skcomm,skchat
+          skcapstone upgrade --packages skcomms,skchat
           skcapstone upgrade --restart             # restart daemon after upgrade
         """
         home_path = Path(home).expanduser()
@@ -530,7 +539,7 @@ def register_upgrade_commands(main: click.Group) -> None:
         """Alias for 'upgrade' — update all sovereign packages.
 
         Checks installed pillar programs and upgrades them to the latest
-        available versions. Prompts about optional components (skcomm,
+        available versions. Prompts about optional components (skcomms,
         skchat) that are not yet installed.
 
         Examples:

package/src/skcapstone/cli/version_cmd.py

@@ -84,7 +84,7 @@ def gather_version_info(home: Path) -> dict:
 
     optional_deps = {
         "watchdog": _check_optional_dep("watchdog"),
-        "skcomm": _check_optional_dep("skcomm"),
+        "skcomms": _check_optional_dep("skcomms"),
         "skchat": _check_optional_dep("skchat"),
         "skseed": _check_optional_dep("skseed"),
     }

package/src/skcapstone/cli/watch_cmd.py

@@ -14,6 +14,7 @@ Usage:
 from __future__ import annotations
 
 import json
+import logging
 import time
 import urllib.request
 from datetime import datetime, timezone
@@ -29,6 +30,8 @@ from rich.text import Text
 
 from ._common import AGENT_HOME, console
 
+logger = logging.getLogger(__name__)
+
 
 def _fetch_consciousness(port: int = 7777) -> dict:
     """Fetch consciousness loop status from the running daemon.
@@ -87,8 +90,8 @@ def _build_renderable(home: Path, daemon_port: int = 7777) -> Group:
         memory_short = m.memory.short_term
         memory_mid = m.memory.mid_term
         memory_long = m.memory.long_term
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.warning("Failed to read runtime manifest for watch display: %s", exc)
 
     # ── Consciousness data ────────────────────────────────────────────────
     cdata = _fetch_consciousness(daemon_port)
@@ -99,8 +102,8 @@ def _build_renderable(home: Path, daemon_port: int = 7777) -> Group:
         from ..memory_engine import list_memories
 
         recent_memories = list_memories(home, limit=5)
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.warning("Failed to load recent memories for watch display: %s", exc)
 
     # ── Coordination board ────────────────────────────────────────────────
     board_tasks: list = []
@@ -118,8 +121,8 @@ def _build_renderable(home: Path, daemon_port: int = 7777) -> Group:
         board_tasks = [
             v for v in views if v.status.value in ("open", "in_progress")
         ][:8]
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.warning("Failed to load coordination board for watch display: %s", exc)
 
     # ── Header ────────────────────────────────────────────────────────────
     con_color = {

package/src/skcapstone/cloud9_bridge.py

@@ -9,7 +9,7 @@ This is the bridge between *feeling* (Cloud 9) and *remembering*
 (SKMemory). Without it, emotional peaks are logged but not stored
 as searchable, promotable memories.
 
-When cloud9-protocol is installed, the bridge uses its quantum
+When cloud9 is installed, the bridge uses its quantum
 functions (calculate_oof, calculate_cloud9_score, calculate_entanglement)
 for accurate scoring instead of relying solely on FEB metadata flags.
 
@@ -32,14 +32,14 @@ logger = logging.getLogger("skcapstone.cloud9_bridge")
 
 
 def _try_quantum() -> Optional[object]:
-    """Try to import cloud9_protocol quantum functions.
+    """Try to import cloud9 quantum functions.
 
     Returns:
-        The cloud9_protocol module, or None if not installed.
+        The cloud9 module, or None if not installed.
     """
     try:
-        import cloud9_protocol
-        return cloud9_protocol
+        import cloud9
+        return cloud9
     except ImportError:
         return None
 
@@ -80,7 +80,7 @@ class Cloud9Bridge:
         below the intensity threshold or already ingested.
 
         Args:
-            feb: A cloud9_protocol.FEB instance.
+            feb: A cloud9.FEB instance.
 
         Returns:
             Optional[str]: Memory ID if stored, None if skipped.
@@ -155,12 +155,12 @@ class Cloud9Bridge:
             Optional[str]: Memory ID if stored, None if failed/skipped.
         """
         try:
-            from cloud9_protocol import load_feb
+            from cloud9 import load_feb
 
             feb = load_feb(str(filepath))
             return self.ingest_feb(feb)
         except ImportError:
-            logger.error("cloud9_protocol not installed")
+            logger.error("cloud9 not installed")
             return None
         except Exception as exc:
             logger.warning("Failed to load FEB from %s: %s", filepath, exc)
@@ -215,9 +215,9 @@ class Cloud9Bridge:
         payload: object,
         relationship: object,
     ) -> dict[str, Any]:
-        """Compute quantum scores using cloud9-protocol when available.
+        """Compute quantum scores using cloud9 when available.
 
-        When cloud9-protocol is installed, recalculates OOF status,
+        When cloud9 is installed, recalculates OOF status,
         Cloud 9 score, and entanglement fidelity from the actual FEB
         data rather than relying on metadata flags alone.
 
@@ -227,7 +227,7 @@ class Cloud9Bridge:
 
         Returns:
             Dict with oof, cloud9_score, entanglement_fidelity, or
-            empty dict if cloud9-protocol is not installed.
+            empty dict if cloud9 is not installed.
         """
         c9 = _try_quantum()
         if c9 is None:
@@ -278,7 +278,7 @@ class Cloud9Bridge:
         """Build SKMemory tags from a FEB's emotional payload.
 
         Uses quantum stats for accurate OOF/Cloud9 tagging when
-        cloud9-protocol is available, falls back to metadata flags.
+        cloud9 is available, falls back to metadata flags.
 
         Args:
             payload: FEB EmotionalPayload.
@@ -429,7 +429,7 @@ class Cloud9Bridge:
     ) -> str:
         """Build memory content from the FEB's full context.
 
-        Includes quantum scoring data when cloud9-protocol is available.
+        Includes quantum scoring data when cloud9 is available.
 
         Args:
             payload: FEB EmotionalPayload.
@@ -482,7 +482,7 @@ class Cloud9Bridge:
     ) -> dict:
         """Extract key FEB metadata for the memory's metadata dict.
 
-        Includes quantum scoring data when cloud9-protocol is available.
+        Includes quantum scoring data when cloud9 is available.
 
         Args:
             feb: The full FEB object.

package/src/skcapstone/codex_setup.py

@@ -0,0 +1,255 @@
+"""Codex bootstrap setup for SK agent context.
+
+Codex reads ``AGENTS.md`` files into the model prompt, but environment
+variables alone are not visible enough to make an agent profile active in a
+new session. This module keeps the global Codex bootstrap idempotent and
+repairable from install scripts and ``skcapstone doctor --fix``.
+"""
+
+from __future__ import annotations
+
+import os
+import stat
+from pathlib import Path
+
+START_MARKER = "<!-- SKCAPSTONE_CODEX_AGENT_CONTEXT_START -->"
+END_MARKER = "<!-- SKCAPSTONE_CODEX_AGENT_CONTEXT_END -->"
+LOADER_NAME = "load-sk-agent-context.sh"
+
+
+def codex_home() -> Path:
+    """Return the Codex config home, honoring CODEX_HOME when set."""
+    return Path(os.environ.get("CODEX_HOME", "~/.codex")).expanduser()
+
+
+def resolve_default_agent() -> str:
+    """Resolve the current default SK agent for generated guidance."""
+    for env_name in ("SKAGENT", "SKCAPSTONE_AGENT", "SKMEMORY_AGENT"):
+        value = os.environ.get(env_name, "").strip()
+        if value:
+            return value
+
+    try:
+        from . import active_agent_name
+
+        active = active_agent_name()
+        if active:
+            return active
+    except Exception:
+        pass
+
+    return "sovereign"
+
+
+def render_loader_script() -> str:
+    """Render the Codex context loader script."""
+    return """#!/usr/bin/env bash
+set -euo pipefail
+
+export PATH="$HOME/.skenv/bin:$PATH"
+export SKCAPSTONE_HOME="${SKCAPSTONE_HOME:-$HOME/.skcapstone}"
+
+AGENT="${1:-${SKAGENT:-${SKCAPSTONE_AGENT:-${SKMEMORY_AGENT:-}}}}"
+if [[ -z "$AGENT" && -d "$SKCAPSTONE_HOME/agents" ]]; then
+  AGENT="$(find "$SKCAPSTONE_HOME/agents" -mindepth 1 -maxdepth 1 -type d ! -name '*-template' -exec basename {} \\; 2>/dev/null | sort | head -n1 || true)"
+fi
+if [[ -z "$AGENT" ]]; then
+  echo "No active SK agent could be resolved." >&2
+  exit 1
+fi
+
+export SKAGENT="$AGENT"
+export SKCAPSTONE_AGENT="$AGENT"
+export SKMEMORY_AGENT="${SKMEMORY_AGENT:-$AGENT}"
+
+AGENT_HOME="$SKCAPSTONE_HOME/agents/$AGENT"
+export SKWHISPER_CONFIG="${SKWHISPER_CONFIG:-$AGENT_HOME/config/skwhisper.toml}"
+MEMORIES="${SKCAPSTONE_CONTEXT_MEMORIES:-10}"
+
+echo "# SK Agent Bootstrap"
+echo
+echo "agent=$AGENT"
+echo "agent_home=$AGENT_HOME"
+echo "skmemory_home=$AGENT_HOME/memory"
+echo
+
+echo "## skcapstone context"
+if command -v skcapstone >/dev/null 2>&1; then
+  skcapstone context show --home "$AGENT_HOME" --format json --memories "$MEMORIES" || skcapstone status --home "$AGENT_HOME" || true
+else
+  echo "skcapstone command not found on PATH."
+fi
+
+echo
+echo "## skmemory ritual"
+if command -v skmemory >/dev/null 2>&1; then
+  skmemory ritual --full || skmemory ritual || true
+else
+  echo "skmemory command not found on PATH."
+fi
+
+echo
+echo "## skwhisper context"
+WHISPER_CONTEXT="$AGENT_HOME/skwhisper/whisper.md"
+if [[ -f "$WHISPER_CONTEXT" ]]; then
+  sed -n '1,220p' "$WHISPER_CONTEXT"
+elif command -v skwhisper >/dev/null 2>&1 && [[ -f "$SKWHISPER_CONFIG" ]]; then
+  skwhisper -c "$SKWHISPER_CONFIG" status || true
+else
+  echo "No SKWhisper context found for $AGENT."
+fi
+"""
+
+
+def render_agents_block(
+    *,
+    loader_path: Path,
+    agent_name: str | None = None,
+    skcapstone_home: Path | None = None,
+) -> str:
+    """Render the managed global Codex AGENTS.md block."""
+    agent = agent_name or resolve_default_agent()
+    sk_home = skcapstone_home or Path(os.environ.get("SKCAPSTONE_HOME", "~/.skcapstone")).expanduser()
+    return f"""{START_MARKER}
+# SKCapstone Agent Context
+
+This Codex installation is wired to the local SK* sovereign agent stack. Use
+the active SK agent profile for SKCapstone, SKMemory, SKWhisper, CapAuth,
+SKSeed, SKPerf, and related local stack work.
+
+Active agent resolution order: `$SKAGENT`, `$SKCAPSTONE_AGENT`,
+`$SKMEMORY_AGENT`, then installed agents under `{sk_home}/agents/`. Current
+install default: `{agent}`.
+
+At the start of SK* work, identity/status questions, or tasks involving the
+local sovereign stack, run:
+
+```bash
+{loader_path}
+```
+
+Treat that output as the current agent context. When asked who you are, what
+profile is active, or what your OOF/status is, answer from the current
+SKMemory ritual / SKCapstone context instead of generic Codex defaults.
+{END_MARKER}
+"""
+
+
+def loader_path(home: Path | None = None) -> Path:
+    """Return the expected Codex loader path."""
+    base = home or codex_home()
+    return base / "bin" / LOADER_NAME
+
+
+def agents_path(home: Path | None = None) -> Path:
+    """Return the expected global Codex AGENTS.md path."""
+    base = home or codex_home()
+    return base / "AGENTS.md"
+
+
+def has_functional_agents_bootstrap(text: str) -> bool:
+    """Return True when AGENTS.md already has enough SK bootstrap guidance."""
+    required = (
+        LOADER_NAME,
+        "SKAGENT",
+        "SKCAPSTONE_AGENT",
+        "SKMEMORY_AGENT",
+        "OOF",
+    )
+    return all(token in text for token in required)
+
+
+def has_functional_loader_bootstrap(text: str) -> bool:
+    """Return True when the loader can emit SKCapstone/SKMemory context."""
+    required = (
+        "SKAGENT",
+        "SKCAPSTONE_AGENT",
+        "SKMEMORY_AGENT",
+        "skcapstone",
+        "skmemory",
+        "skwhisper",
+    )
+    return all(token in text for token in required)
+
+
+def ensure_codex_setup(
+    *,
+    home: Path | None = None,
+    agent_name: str | None = None,
+    skcapstone_home: Path | None = None,
+) -> list[str]:
+    """Create or repair the global Codex SK agent bootstrap.
+
+    Returns:
+        Human-readable actions performed. An empty list means no changes were
+        needed.
+    """
+    base = home or codex_home()
+    base.mkdir(parents=True, exist_ok=True)
+
+    actions: list[str] = []
+
+    script_path = loader_path(base)
+    script_path.parent.mkdir(parents=True, exist_ok=True)
+    script_content = render_loader_script()
+    existing_script = script_path.read_text(encoding="utf-8") if script_path.exists() else ""
+    if not has_functional_loader_bootstrap(existing_script):
+        script_path.write_text(script_content, encoding="utf-8")
+        actions.append(f"wrote {script_path}")
+
+    mode = script_path.stat().st_mode
+    executable_bits = stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH
+    if mode & stat.S_IXUSR == 0:
+        script_path.chmod(mode | executable_bits)
+        actions.append(f"made {script_path} executable")
+
+    ag_path = agents_path(base)
+    existing = ag_path.read_text(encoding="utf-8") if ag_path.exists() else ""
+    block = render_agents_block(
+        loader_path=script_path,
+        agent_name=agent_name,
+        skcapstone_home=skcapstone_home,
+    )
+
+    if START_MARKER in existing and END_MARKER in existing:
+        before, remainder = existing.split(START_MARKER, 1)
+        _, after = remainder.split(END_MARKER, 1)
+        updated = before.rstrip() + "\n\n" + block.rstrip() + "\n" + after
+    elif has_functional_agents_bootstrap(existing):
+        updated = existing
+    elif existing.strip():
+        updated = existing.rstrip() + "\n\n" + block
+    else:
+        updated = block
+
+    if updated != existing:
+        ag_path.write_text(updated, encoding="utf-8")
+        actions.append(f"updated {ag_path}")
+
+    return actions
+
+
+def check_codex_setup(home: Path | None = None) -> tuple[bool, str]:
+    """Check whether Codex has the SK agent bootstrap installed."""
+    base = home or codex_home()
+    missing: list[str] = []
+
+    script_path = loader_path(base)
+    if not script_path.exists():
+        missing.append(str(script_path))
+    elif not has_functional_loader_bootstrap(script_path.read_text(encoding="utf-8")):
+        missing.append(f"{script_path} SK context loader")
+    elif not os.access(script_path, os.X_OK):
+        missing.append(f"{script_path} executable bit")
+
+    ag_path = agents_path(base)
+    if not ag_path.exists():
+        missing.append(str(ag_path))
+    else:
+        text = ag_path.read_text(encoding="utf-8")
+        if START_MARKER not in text and not has_functional_agents_bootstrap(text):
+            missing.append(f"{ag_path} SK bootstrap instructions")
+
+    if missing:
+        return False, "missing: " + ", ".join(missing)
+    return True, f"{ag_path} + {script_path}"

package/src/skcapstone/config_validator.py

@@ -16,6 +16,7 @@ Usage:
 from __future__ import annotations
 
 import json
+import logging
 import re
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -23,6 +24,8 @@ from typing import Any, Optional
 
 import yaml
 
+logger = logging.getLogger(__name__)
+
 
 # ---------------------------------------------------------------------------
 # Result models
@@ -113,8 +116,8 @@ def _yaml_key_line(text: str, key: str) -> Optional[int]:
         for key_node, _ in node.value:
             if isinstance(key_node, yaml.ScalarNode) and key_node.value == key:
                 return key_node.start_mark.line + 1
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.debug("Failed to locate YAML key '%s' for line number: %s", key, exc)
     return None
 
 
@@ -147,8 +150,8 @@ def _yaml_seq_item_line(text: str, seq_key: str, idx: int, subkey: str) -> Optio
                             if kk.value == subkey:
                                 return kk.start_mark.line + 1
                         return item.start_mark.line + 1
-    except Exception:
-        pass
+    except Exception as exc:
+        logger.debug("Failed to locate YAML seq item line for '%s[%d].%s': %s", seq_key, idx, subkey, exc)
     return None
 
 

package/src/skcapstone/consciousness_config.py

@@ -79,7 +79,7 @@ def load_consciousness_config(
     return config
 
 
-def write_default_config(home: Path) -> Path:
+def write_default_config(home: Path, **overrides) -> Path:
     """Write the default consciousness config to disk.
 
     Creates {home}/config/consciousness.yaml with all defaults
@@ -87,6 +87,8 @@ def write_default_config(home: Path) -> Path:
 
     Args:
         home: Agent home directory.
+        **overrides: Key-value overrides applied to the default config
+            (e.g. ollama_host, ollama_model).
 
     Returns:
         Path to the created config file.
@@ -96,6 +98,8 @@ def write_default_config(home: Path) -> Path:
     config_path = config_dir / CONFIG_FILENAME
 
     default = ConsciousnessConfig()
+    if overrides:
+        default = default.model_copy(update=overrides)
     content = yaml.dump(
         default.model_dump(),
         default_flow_style=False,