coding-os 0.3.21__tar.gz → 0.3.22__tar.gz

{coding_os-0.3.21 → coding_os-0.3.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: coding-os
-Version: 0.3.21
+Version: 0.3.22
 Summary: The cognitive operating system that gives AI agents memory, structure, and discipline
 Author-email: Kourosh Ebrahimzadeh <info@coding-os.dev>
 License-Expression: Apache-2.0
@@ -611,6 +611,11 @@ public checkouts, 8 on this one (`min` in brackets — the honest worst case):
 | django/django @ 5.2 | 2,818 | **76.8%** (50.3) | 70.8% (18.5) | **77.1%** (51.1) |
 | this repo | 3,317 | **79.7%** (65.9) | 74.0% (64.7) | **79.7%** (65.7) |
 
+Every number below is a **token cost**. The harness measures what each approach
+spends, not whether its answer is better; it emits no accuracy metric and has not
+been run against a code-retrieval benchmark. Read the tables as a cost result and
+nothing more ([limits](docs/engineering/third-party-token-bench.md#honest-limits)).
+
 Read it as three findings, including the one that does not flatter us:
 
 1. **"Who calls this?" and "what does a rename touch?" are a consistent ~75–82%

{coding_os-0.3.21 → coding_os-0.3.22}/README.md

@@ -544,6 +544,11 @@ public checkouts, 8 on this one (`min` in brackets — the honest worst case):
 | django/django @ 5.2 | 2,818 | **76.8%** (50.3) | 70.8% (18.5) | **77.1%** (51.1) |
 | this repo | 3,317 | **79.7%** (65.9) | 74.0% (64.7) | **79.7%** (65.7) |
 
+Every number below is a **token cost**. The harness measures what each approach
+spends, not whether its answer is better; it emits no accuracy metric and has not
+been run against a code-retrieval benchmark. Read the tables as a cost result and
+nothing more ([limits](docs/engineering/third-party-token-bench.md#honest-limits)).
+
 Read it as three findings, including the one that does not flatter us:
 
 1. **"Who calls this?" and "what does a rename touch?" are a consistent ~75–82%

{coding_os-0.3.21 → coding_os-0.3.22}/coding_os.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: coding-os
-Version: 0.3.21
+Version: 0.3.22
 Summary: The cognitive operating system that gives AI agents memory, structure, and discipline
 Author-email: Kourosh Ebrahimzadeh <info@coding-os.dev>
 License-Expression: Apache-2.0
@@ -611,6 +611,11 @@ public checkouts, 8 on this one (`min` in brackets — the honest worst case):
 | django/django @ 5.2 | 2,818 | **76.8%** (50.3) | 70.8% (18.5) | **77.1%** (51.1) |
 | this repo | 3,317 | **79.7%** (65.9) | 74.0% (64.7) | **79.7%** (65.7) |
 
+Every number below is a **token cost**. The harness measures what each approach
+spends, not whether its answer is better; it emits no accuracy metric and has not
+been run against a code-retrieval benchmark. Read the tables as a cost result and
+nothing more ([limits](docs/engineering/third-party-token-bench.md#honest-limits)).
+
 Read it as three findings, including the one that does not flatter us:
 
 1. **"Who calls this?" and "what does a rename touch?" are a consistent ~75–82%

{coding_os-0.3.21 → coding_os-0.3.22}/coding_os.egg-info/SOURCES.txt

@@ -109,6 +109,7 @@ src/cli/_skill_project.py
 src/cli/_stack_parsers.py
 src/cli/_stack_relocation.py
 src/cli/_update_manifest.py
+src/cli/_yaml_edit.py
 src/cli/adapter_registry.py
 src/cli/add_stack.py
 src/cli/adopt_command.py
@@ -380,6 +381,7 @@ src/core/hooks/enforce-doc-anchor.sh
 src/core/hooks/enforce-doc-sync.sh
 src/core/hooks/enforce-graph-context.sh
 src/core/hooks/enforce-graph-first-read.sh
+src/core/hooks/enforce-humanizer-audit.sh
 src/core/hooks/enforce-memory-check.sh
 src/core/hooks/enforce-rename-plan.sh
 src/core/hooks/enforce-scaffold-boundary.sh
@@ -400,6 +402,7 @@ src/core/hooks/lint-task.sh
 src/core/hooks/nudge-docs-first.sh
 src/core/hooks/nudge-git-mode.sh
 src/core/hooks/nudge-graph-os.sh
+src/core/hooks/nudge-humanizer.sh
 src/core/hooks/nudge-learn-narrative.sh
 src/core/hooks/nudge-model-routing.sh
 src/core/hooks/nudge-reentry.sh
@@ -613,6 +616,10 @@ src/core/skills/hexagonal-architecture/references/anti-patterns.md
 src/core/skills/hexagonal-architecture/references/go-fiber-layout.md
 src/core/skills/hexagonal-architecture/references/python-fastapi-layout.md
 src/core/skills/hexagonal-architecture/references/react-native-layout.md
+src/core/skills/humanizer/NOTICE
+src/core/skills/humanizer/SKILL.md
+src/core/skills/humanizer/references/false-positives.md
+src/core/skills/humanizer/references/patterns.md
 src/core/skills/i18n/SKILL.md
 src/core/skills/incident-response/SKILL.md
 src/core/skills/incident-response/assets/incident-checklist.md
@@ -924,7 +931,7 @@ src/core/web/ui/dist/cos-board-tokens.css
 src/core/web/ui/dist/favicon.png
 src/core/web/ui/dist/index.html
 src/core/web/ui/dist/assets/graph-BbrS1Nv2.js
-src/core/web/ui/dist/assets/index-C1-FjUpV.js
+src/core/web/ui/dist/assets/index-D-AKdP4m.js
 src/core/web/ui/dist/assets/index-qIBSb3Dw.css
 src/core/web/ui/dist/assets/logo-C_DJT4rG.png
 src/core/web/ui/dist/assets/rolldown-runtime-Dd_uD5pT.js

{coding_os-0.3.21 → coding_os-0.3.22}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "coding-os"
-version = "0.3.21"
+version = "0.3.22"
 description = "The cognitive operating system that gives AI agents memory, structure, and discipline"
 readme = "README.md"
 requires-python = ">=3.10"

{coding_os-0.3.21 → coding_os-0.3.22}/src/adapters/claude/_claude_sdk_options.py

@@ -314,19 +314,25 @@ def _formula_prompts(request: Any, system_prompt_body: str) -> tuple[dict[str, A
 
 
 def _structured_output_format(agent_meta: Any, formula_id: str) -> dict[str, Any] | None:
-    # Structured output (T1) — opt-in per role via
-    # `structured_output: true` frontmatter. SDK enforces the
-    # schema and surfaces failures as
-    # subtype="error_max_structured_output_retries".
-    if not (isinstance(agent_meta, dict) and agent_meta.get("structured_output")):
+    # The declared `output_schema` is the opt-in. It used to take a second
+    # `structured_output: true` flag as well, and ten of the fifteen roles
+    # declared a schema without it — so the SDK never enforced anything and the
+    # mismatch surfaced at persistence time, after the run was billed. A role
+    # that declares a schema means it; `structured_output: false` is the
+    # explicit opt-out for one that wants free-form generation anyway.
+    # Enforcement failures arrive as subtype="error_max_structured_output_retries".
+    if not isinstance(agent_meta, dict):
+        return None
+    if agent_meta.get("structured_output") is False:
         return None
     schema = _resolve_output_schema(agent_meta)
     if schema is None:
-        logger.warning(
-            "role %s requested structured_output but schema could not be "
-            "resolved — falling back to regex extraction",
-            formula_id,
-        )
+        if agent_meta.get("structured_output"):
+            logger.warning(
+                "role %s requested structured_output but schema could not be "
+                "resolved — falling back to regex extraction",
+                formula_id,
+            )
         return None
     return {"type": "json_schema", "schema": schema}
 

{coding_os-0.3.21 → coding_os-0.3.22}/src/adapters/claude/settings.template.json

@@ -700,6 +700,11 @@
             "command": "env COS_AGENT=claude \"{{HOOKS_DIR}}/nudge-graph-os.sh\"",
             "timeout": 10
           },
+          {
+            "type": "command",
+            "command": "env COS_AGENT=claude \"{{HOOKS_DIR}}/nudge-humanizer.sh\"",
+            "timeout": 10
+          },
           {
             "type": "command",
             "command": "env COS_AGENT=claude \"{{HOOKS_DIR}}/nudge-model-routing.sh\"",
@@ -748,6 +753,11 @@
       {
         "matcher": "",
         "hooks": [
+          {
+            "type": "command",
+            "command": "env COS_AGENT=claude \"{{HOOKS_DIR}}/enforce-humanizer-audit.sh\"",
+            "timeout": 10
+          },
           {
             "type": "command",
             "command": "env COS_AGENT=claude \"{{HOOKS_DIR}}/drain-embedding-outbox.sh\"",

{coding_os-0.3.21 → coding_os-0.3.22}/src/adapters/codex/adapter.yaml

@@ -262,6 +262,7 @@ hook_dispatchers:
     status_message: "📝 Finalizing session recap + memory enrichment..."
     timeout: 5000
     delegates:
+      - enforce-humanizer-audit.sh
       - session-end.sh
       - warn-abandoned-task.sh
       - nudge-learn-narrative.sh
@@ -318,6 +319,7 @@ hook_dispatchers:
       - auto-compose-roles.sh
       - classify-task-mode.sh
       - nudge-graph-os.sh
+      - nudge-humanizer.sh
       - nudge-model-routing.sh
       - resolve-supervise-route.sh
       - nudge-git-mode.sh

{coding_os-0.3.21 → coding_os-0.3.22}/src/adapters/codex/hooks/codex-stop-dispatch.sh

@@ -56,7 +56,10 @@ run_delegate() {
   return 0
 }
 
-for delegate in session-end.sh warn-abandoned-task.sh nudge-learn-narrative.sh check-capture-worked.sh auto-trace-rotate.sh snapshot-transcript.sh drain-embedding-outbox.sh agent-presence.sh; do
+# enforce-humanizer-audit runs first: it is the only blocking delegate here,
+# and a gate that fires after the session recap would make every blocked turn
+# write its telemetry twice.
+for delegate in enforce-humanizer-audit.sh session-end.sh warn-abandoned-task.sh nudge-learn-narrative.sh check-capture-worked.sh auto-trace-rotate.sh snapshot-transcript.sh drain-embedding-outbox.sh agent-presence.sh; do
   run_delegate "$delegate"
 done
 

{coding_os-0.3.21 → coding_os-0.3.22}/src/adapters/codex/hooks/codex-userpromptsubmit-dispatch.sh

@@ -57,6 +57,7 @@ for delegate in \
   auto-compose-roles.sh \
   classify-task-mode.sh \
   nudge-graph-os.sh \
+  nudge-humanizer.sh \
   nudge-model-routing.sh \
   resolve-supervise-route.sh \
   nudge-git-mode.sh \

{coding_os-0.3.21 → coding_os-0.3.22}/src/cli/_doctor_runtime.py

@@ -81,6 +81,34 @@ DATABASE_SIZE_BUDGET_MEGABYTES = 200
 WRITE_AHEAD_LOG_BUDGET_MEGABYTES = 50
 
 
+def _wal_recovery_step(write_ahead_log_path: Path, write_ahead_log_bytes: int) -> str:
+    # A WAL only ever grows past its budget because something is blocking the
+    # checkpoint, and that is exactly when the volume is least likely to have
+    # room: the 59 GB WAL that motivated this check sat on a volume with less
+    # free space than the WAL itself. TRUNCATE folds every frame into the main
+    # DB in one pass, so recommending it blind is how a recovery step turns a
+    # full disk into a failed write. Measure first, then name a step that fits.
+    try:
+        free_bytes = shutil.disk_usage(write_ahead_log_path.parent).free
+    except OSError as exc:
+        logger.debug("disk_usage failed for %s: %s", write_ahead_log_path.parent, exc)
+        return "checkpoint: sqlite3 coding-os.db 'PRAGMA wal_checkpoint(TRUNCATE)'"
+
+    if free_bytes > write_ahead_log_bytes:
+        return "checkpoint: sqlite3 coding-os.db 'PRAGMA wal_checkpoint(TRUNCATE)'"
+
+    free_megabytes = free_bytes / (1024 * 1024)
+    wal_megabytes = write_ahead_log_bytes / (1024 * 1024)
+    return (
+        f"do NOT run wal_checkpoint(TRUNCATE): {free_megabytes:.0f} MB free is less "
+        f"than the {wal_megabytes:.0f} MB WAL, so folding it into the DB can fail "
+        "mid-write. Drain incrementally instead — repeat "
+        "\"sqlite3 coding-os.db 'PRAGMA wal_checkpoint(PASSIVE)'\" until it reports "
+        "0 pages, closing long-lived readers (cos hub stop, MCP clients) between "
+        "passes; then free space and TRUNCATE."
+    )
+
+
 def _check_runtime_state_within_budget(project: Path, report: DoctorReport) -> None:
     """state.size_within_budget — coding-os.db and its WAL stay within size budgets."""
     database_path = project / DATABASE_FILE_RELATIVE_PATH
@@ -100,14 +128,15 @@ def _check_runtime_state_within_budget(project: Path, report: DoctorReport) -> N
             )
 
     if write_ahead_log_path.exists():
-        write_ahead_log_megabytes = write_ahead_log_path.stat().st_size / (1024 * 1024)
+        write_ahead_log_bytes = write_ahead_log_path.stat().st_size
+        write_ahead_log_megabytes = write_ahead_log_bytes / (1024 * 1024)
         if write_ahead_log_megabytes > WRITE_AHEAD_LOG_BUDGET_MEGABYTES:
             findings.append(
                 {
                     "file": WRITE_AHEAD_LOG_RELATIVE_PATH,
                     "actual_megabytes": round(write_ahead_log_megabytes, 1),
                     "budget_megabytes": WRITE_AHEAD_LOG_BUDGET_MEGABYTES,
-                    "fix": "checkpoint: sqlite3 coding-os.db 'PRAGMA wal_checkpoint(TRUNCATE)'",
+                    "fix": _wal_recovery_step(write_ahead_log_path, write_ahead_log_bytes),
                 }
             )
 

{coding_os-0.3.21 → coding_os-0.3.22}/src/cli/_skill_project.py

@@ -17,6 +17,7 @@ from pathlib import Path
 import click
 
 from cli._resources import core_dir, templates_dir
+from cli._yaml_edit import add_list_item, remove_list_item
 
 
 def user_skills_dir() -> Path:
@@ -52,14 +53,6 @@ def _load_project_config(project_root: Path) -> dict:
     return yaml.safe_load(_project_config_path(project_root).read_text(encoding="utf-8")) or {}
 
 
-def _save_project_config(project_root: Path, config: dict) -> None:
-    import yaml
-
-    _project_config_path(project_root).write_text(
-        yaml.dump(config, sort_keys=False, allow_unicode=True), encoding="utf-8"
-    )
-
-
 def _installed_adapter_skills_dirs(project_root: Path) -> list[Path]:
     from cli._resources import adapters_dir
     from cli.adapter_registry import load_adapter_registry
@@ -76,6 +69,10 @@ def _installed_adapter_skills_dirs(project_root: Path) -> list[Path]:
 
 _SKILL_NAME_RE = re.compile(r"^[A-Za-z0-9][A-Za-z0-9._-]*$")
 
+# Subdirectories a SKILL.md may link by relative path. Kept in sync with
+# install-adapter.sh and link-stack-skills.sh, which project the same set.
+SKILL_COMPANION_DIRS = ("references", "assets", "scripts")
+
 
 def _known_skill_provenance(name: str) -> str | None:
     """'core' | 'stack' | 'community' | None — where this skill name resolves."""
@@ -111,24 +108,32 @@ def _skill_source_skill_md(name: str, provenance: str) -> Path | None:
 def _relink_core_stack_skill(
     project_root: Path, name: str, source_skill_md: Path, *, link: bool
 ) -> int:
-    """Re-link (or unlink) a core/stack skill's SKILL.md in every installed
-    adapter skills dir. Returns links touched. Linked as
-    `<skills_dir>/<name>/SKILL.md` (parity with install-adapter.sh step 6)."""
+    """Re-link (or unlink) a core/stack skill in every installed adapter skills
+    dir. Returns links touched. Linked as `<skills_dir>/<name>/SKILL.md` plus one
+    symlink per companion dir (parity with install-adapter.sh step 6)."""
     touched = 0
+    source_dir = source_skill_md.parent
     for skills_root in _installed_adapter_skills_dirs(project_root):
         skill_dir = skills_root / name
-        link_path = skill_dir / "SKILL.md"
-        if link:
-            skill_dir.mkdir(parents=True, exist_ok=True)
-            if link_path.is_symlink() and not link_path.exists():
-                link_path.unlink()  # dangling link (target moved) — clear before relink
-            if not link_path.exists():
-                link_path.symlink_to(source_skill_md)
-                touched += 1
-        else:
-            if link_path.is_symlink() or link_path.exists():
+        # A SKILL.md links its companion dirs by relative path. Without them the
+        # consumer gets a skill whose every reference dangles.
+        targets = [(skill_dir / "SKILL.md", source_skill_md)] + [
+            (skill_dir / sub, source_dir / sub)
+            for sub in SKILL_COMPANION_DIRS
+            if (source_dir / sub).is_dir()
+        ]
+        for link_path, source in targets:
+            if link:
+                skill_dir.mkdir(parents=True, exist_ok=True)
+                if link_path.is_symlink() and not link_path.exists():
+                    link_path.unlink()  # dangling link (target moved) — clear before relink
+                if not link_path.exists():
+                    link_path.symlink_to(source)
+                    touched += 1
+            elif link_path.is_symlink() or link_path.exists():
                 link_path.unlink()
                 touched += 1
+        if not link:
             # dir not empty / absent — leave it
             with contextlib.suppress(OSError):
                 skill_dir.rmdir()
@@ -183,36 +188,29 @@ def set_project_skill(project_root: Path, name: str, enabled: bool) -> dict:
     config = _load_project_config(project_root)
     extras = list(config.get("extra_skills") or [])
     disabled = list(config.get("disabled_skills") or [])
-    stack_skills = _installed_stack_skills(config)
     source = _skill_source_skill_md(name, provenance)
 
     # Community skills are opt-IN via extras; core/stack ship by default and are
     # opt-OUT via the disabled list. The two lists are mutually exclusive per id.
     if provenance == "community":
-        if enabled:
-            if name in extras:
-                return {
-                    "name": name,
-                    "provenance": provenance,
-                    "changed": False,
-                    "note": "already enabled",
-                }
-            extras.append(name)
-        else:
-            if name not in extras:
-                raise click.ClickException(f"'{name}' is not an extra skill of this project")
-            extras.remove(name)
+        if enabled and name in extras:
+            return {
+                "name": name,
+                "provenance": provenance,
+                "changed": False,
+                "note": "already enabled",
+            }
+        if not enabled and name not in extras:
+            raise click.ClickException(f"'{name}' is not an extra skill of this project")
     else:  # core | stack
-        if enabled:
-            if name not in disabled:
-                return {
-                    "name": name,
-                    "provenance": provenance,
-                    "changed": False,
-                    "note": "already enabled (core/stack skills ship by default)",
-                }
-            disabled.remove(name)
-        else:
+        if enabled and name not in disabled:
+            return {
+                "name": name,
+                "provenance": provenance,
+                "changed": False,
+                "note": "already enabled (core/stack skills ship by default)",
+            }
+        if not enabled:
             if name in disabled:
                 return {
                     "name": name,
@@ -221,15 +219,20 @@ def set_project_skill(project_root: Path, name: str, enabled: bool) -> dict:
                     "note": "already disabled",
                 }
             # A stack skill not installed by any current stack cannot be disabled.
-            if provenance == "stack" and name not in stack_skills:
+            if provenance == "stack" and name not in _installed_stack_skills(config):
                 raise click.ClickException(
                     f"'{name}' is a stack skill but no installed stack provides it"
                 )
-            disabled.append(name)
 
-    config["extra_skills"] = extras
-    config["disabled_skills"] = sorted(disabled)
-    _save_project_config(project_root, config)
+    # Splice the one changed item rather than dumping the parsed config back:
+    # a round-trip drops every comment the operator wrote.
+    list_key = "extra_skills" if provenance == "community" else "disabled_skills"
+    is_append = enabled if provenance == "community" else not enabled
+    splice = add_list_item if is_append else remove_list_item
+    config_path = _project_config_path(project_root)
+    config_path.write_text(
+        splice(config_path.read_text(encoding="utf-8"), list_key, name), encoding="utf-8"
+    )
 
     if provenance == "community":
         links_touched = _relink_community_skill(project_root, name, link=enabled)

coding_os-0.3.22/src/cli/_yaml_edit.py

@@ -0,0 +1,79 @@
+"""Comment-preserving list edits on a project's `.coding-os.yaml`.
+
+A `yaml.dump` round-trip reserializes the whole document and deletes every
+comment the operator wrote, so a one-item change is spliced into the text
+instead. Spec: docs/engineering/skill-architecture.md § Per-project extras.
+"""
+
+from __future__ import annotations
+
+import re
+
+_ITEM_RE = re.compile(r"^(?P<indent>\s*)-\s+(?P<val>.+?)\s*$")
+_EMPTY_INLINE_RE = re.compile(r"^[^\s:]+:\s*\[\s*\]\s*(#.*)?$")
+_DEFAULT_INDENT = "  "
+
+
+def _find_header(lines: list[str], key: str) -> int | None:
+    pattern = re.compile(rf"^{re.escape(key)}:\s*(\[\s*\]\s*)?(#.*)?$")
+    for i, line in enumerate(lines):
+        if pattern.match(line.rstrip("\n")):
+            return i
+    return None
+
+
+def _last_item(lines: list[str], header: int) -> tuple[int, str] | None:
+    """Index and indent of the block's final `- item` line, or None if empty."""
+    found: tuple[int, str] | None = None
+    for j in range(header + 1, len(lines)):
+        body = lines[j].rstrip("\n")
+        if body.strip() == "" or body.startswith("#"):
+            continue
+        match = _ITEM_RE.match(body)
+        if match is None:
+            break
+        found = (j, match.group("indent") or _DEFAULT_INDENT)
+    return found
+
+
+def add_list_item(raw: str, key: str, item: str) -> str:
+    """Append `item` to the top-level list `key`, creating the block if absent."""
+    lines = raw.splitlines(keepends=True)
+    header = _find_header(lines, key)
+    if header is None:
+        suffix = "" if raw == "" or raw.endswith("\n") else "\n"
+        return f"{raw}{suffix}{key}:\n{_DEFAULT_INDENT}- {item}\n"
+
+    if _EMPTY_INLINE_RE.match(lines[header].rstrip("\n")):
+        lines[header] = f"{key}:\n"
+
+    last = _last_item(lines, header)
+    at, indent = (last[0] + 1, last[1]) if last else (header + 1, _DEFAULT_INDENT)
+    lines.insert(at, f"{indent}- {item}\n")
+    return "".join(lines)
+
+
+def remove_list_item(raw: str, key: str, item: str) -> str:
+    """Drop `item` from the top-level list `key`; a no-op when it is absent.
+
+    Removing the block's last item drops the now-empty `key:` header too, so an
+    add/remove pair leaves the file byte-identical instead of accreting a bare
+    key. Absent and empty read the same to every consumer (`… or []`).
+    """
+    lines = raw.splitlines(keepends=True)
+    header = _find_header(lines, key)
+    if header is None:
+        return raw
+    for j in range(header + 1, len(lines)):
+        body = lines[j].rstrip("\n")
+        if body.strip() == "" or body.startswith("#"):
+            continue
+        match = _ITEM_RE.match(body)
+        if match is None:
+            break
+        if match.group("val").strip().strip("'\"") == item:
+            del lines[j]
+            break
+    if _last_item(lines, header) is None and lines[header].rstrip("\n") == f"{key}:":
+        del lines[header]
+    return "".join(lines)

{coding_os-0.3.21 → coding_os-0.3.22}/src/cli/install_commands.py

@@ -212,8 +212,13 @@ def materialize(project_dir: str) -> None:
     """Convert coding-os symlinks to real files (self-contained project)."""
     project = _resolve_project_dir(project_dir)
     materialized = 0
+    dir_links: list[Path] = []
 
-    for root, _dirs, files in os.walk(project):
+    for root, dirs, files in os.walk(project):
+        # os.walk never descends a symlinked directory, so a skill's
+        # references/ link survives a files-only pass. Collect them and replace
+        # them after the walk rather than mutating the tree mid-iteration.
+        dir_links += [p for d in dirs if (p := Path(root) / d).is_symlink()]
         for name in files:
             filepath = Path(root) / name
             if filepath.is_symlink():
@@ -225,6 +230,13 @@ def materialize(project_dir: str) -> None:
                     if materialized % 50 == 0:
                         click.echo(f"  … materialized {materialized} symlinks so far", err=True)
 
+    for dirpath in dir_links:
+        target = dirpath.resolve()
+        if target.is_dir():
+            dirpath.unlink()
+            shutil.copytree(target, dirpath, symlinks=False)
+            materialized += 1
+
     click.echo(f"Materialized {materialized} symlinks to real files.")
     click.echo("Project is now self-contained.")
 
@@ -259,9 +271,11 @@ def eject(project_dir: str, yes: bool) -> None:
     project = _resolve_project_dir(project_dir)
     state_dir = project / STATE_DIR
     config = project / CONFIG_FILE
+    # Directories are walked too: a skill's references/ is a symlink to a dir,
+    # and a files-only sweep leaves it pointing into the meta-repo after eject.
     coding_os_links = [
         p
-        for p in (Path(root) / n for root, _d, fs in os.walk(project) for n in fs)
+        for p in (Path(root) / n for root, ds, fs in os.walk(project) for n in (*ds, *fs))
         if p.is_symlink() and _is_coding_os_symlink(p)
     ]
     # An adapter's root entrypoint is a generated symlink to AGENTS.md; it

{coding_os-0.3.21 → coding_os-0.3.22}/src/core/board_os/sync.py

@@ -71,7 +71,7 @@ def _upsert_task(
     deps_json = json.dumps(list(parsed.depends_on))
     blocked_by_json = json.dumps(list(parsed.blocked_by))
     references_json = json.dumps(list(parsed.references))
-    created_at = parsed.created or datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S")
+    created_at = parsed.created or datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     conn.execute(
         """
         INSERT INTO tasks (
@@ -102,7 +102,7 @@ def _upsert_task(
             references_json = excluded.references_json,
             external_ref    = excluded.external_ref,
             created_at      = COALESCE(tasks.created_at, excluded.created_at),
-            updated_at      = CURRENT_TIMESTAMP
+            updated_at      = strftime('%Y-%m-%dT%H:%M:%SZ', 'now')
         """,
         (
             parsed.task_id,

{coding_os-0.3.21 → coding_os-0.3.22}/src/core/doctor-config.yaml

@@ -22,7 +22,7 @@ placeholder_scan:
   - docs/_meta
   - docs/tasks
 schema:
-  expected_version: 53
+  expected_version: 54
   expected_tables:
   - adapter_health
   - agent_metrics

{coding_os-0.3.21 → coding_os-0.3.22}/src/core/hooks/_cos_env_state.sh

@@ -308,17 +308,21 @@ cos_panel_upgrade_from_payload() {
   # reader that goes through $COS_SESSION_FILE (the SSOT for "who am I")
   # sees an empty value, and the per-session ownership check rejects every
   # state file as un-owned — the cascade that surfaces as banner ses=? ·
-  # task=none · gate=unset on hooks that only have agent-level legacy
-  # state. SessionStart:startup writes a `ses-<agent>-<ts>-<rand>` id; for
-  # resume/compact/user-prompt-submit (where startup never fires for this
-  # panel), we mirror the agent-level session-id when present, else seed
-  # with the panel id (stable across the conversation).
+  # task=none · gate=unset on hooks that only have agent-level legacy state.
+  #
+  # The seed is always NEW. This used to mirror $COS_AGENT_DIR/session-id when
+  # that file existed, on the theory that a resumed conversation should keep
+  # its id. But that file is agent-level: it holds whichever panel wrote last
+  # and nothing ever rotates it, so every panel that starts without a startup
+  # event copied the same value. Observed in the wild: two live panels both
+  # stamped ses-claude-20260527-151803-0b9f, an id minted three and a half
+  # months earlier — colliding `ses=` tails in the banner, and session-keyed
+  # state reaching back to a conversation nobody remembers. A panel with no id
+  # of its own IS a new panel; _session_pulse.sh already refuses that fossil
+  # ("NEVER fall back to $COS_AGENT_DIR/session-id"), and this is its twin.
   if [[ ! -s "$COS_SESSION_FILE" ]]; then
-    local seed=""
-    if [[ -s "${COS_AGENT_DIR}/session-id" ]]; then
-      seed="$(tr -d '\n\r' < "${COS_AGENT_DIR}/session-id" 2>/dev/null || true)"
-    fi
-    [[ -z "$seed" ]] && seed="ses-${COS_AGENT}-${COS_PANEL_ID}"
+    local seed
+    seed="$(cos_mint_session_id)"
     local _tmp="${COS_SESSION_FILE}.tmp.$$"
     printf '%s\n' "$seed" > "$_tmp" 2>/dev/null \
       && mv -f "$_tmp" "$COS_SESSION_FILE" 2>/dev/null \
@@ -326,6 +330,26 @@ cos_panel_upgrade_from_payload() {
   fi
 }
 
+# ---------------------------------------------------------------------------
+# cos_mint_session_id
+#
+# The one place the `ses-<agent>-YYYYMMDD-HHMMSS-xxxx` shape is written.
+# session-context.sh mints one on SessionStart:startup and this helper mints
+# one for a panel that first appears on resume/compact — two writers, one
+# format, so a reader parsing the tail never meets a second shape. Falls back
+# to the panel id (already unique per conversation) when /dev/urandom or xxd
+# is unavailable.
+# ---------------------------------------------------------------------------
+cos_mint_session_id() {
+  local rand
+  rand="$(head -c 4 /dev/urandom 2>/dev/null | xxd -p 2>/dev/null | head -c 4 || true)"
+  if [[ -z "$rand" ]]; then
+    printf 'ses-%s-%s' "${COS_AGENT}" "${COS_PANEL_ID}"
+    return 0
+  fi
+  printf 'ses-%s-%s-%s' "${COS_AGENT}" "$(date +%Y%m%d-%H%M%S)" "$rand"
+}
+
 # ---------------------------------------------------------------------------
 # cos_task_bound_in_live_sibling <task-id>
 #