psyclaw 0.27.22 → 0.28.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1048) hide show
  1. package/README.md +11 -5
  2. package/dist/apps/panel/index.html +2 -2
  3. package/dist/src/adapters/pi/extension.js +225 -92
  4. package/dist/src/adapters/pi/extension.js.map +1 -1
  5. package/dist/src/agents/import.js +44 -32
  6. package/dist/src/agents/import.js.map +1 -1
  7. package/dist/src/analysis/hooks.d.ts +1 -0
  8. package/dist/src/analysis/hooks.js +20 -1
  9. package/dist/src/analysis/hooks.js.map +1 -1
  10. package/dist/src/ars/bridge.d.ts +20 -0
  11. package/dist/src/ars/bridge.js +132 -0
  12. package/dist/src/ars/bridge.js.map +1 -0
  13. package/dist/src/ars/contracts.d.ts +55 -0
  14. package/dist/src/ars/contracts.js +2 -0
  15. package/dist/src/ars/contracts.js.map +1 -0
  16. package/dist/src/ars/panel-plan.d.ts +4 -0
  17. package/dist/src/ars/panel-plan.js +11 -0
  18. package/dist/src/ars/panel-plan.js.map +1 -0
  19. package/dist/src/ars/pi-panel-executor.d.ts +30 -0
  20. package/dist/src/ars/pi-panel-executor.js +140 -0
  21. package/dist/src/ars/pi-panel-executor.js.map +1 -0
  22. package/dist/src/ars/profile.d.ts +36 -0
  23. package/dist/src/ars/profile.js +119 -0
  24. package/dist/src/ars/profile.js.map +1 -0
  25. package/dist/src/ars/re-review.d.ts +22 -0
  26. package/dist/src/ars/re-review.js +172 -0
  27. package/dist/src/ars/re-review.js.map +1 -0
  28. package/dist/src/branding.d.ts +2 -4
  29. package/dist/src/branding.js +3 -5
  30. package/dist/src/branding.js.map +1 -1
  31. package/dist/src/bundled-tools.d.ts +3 -0
  32. package/dist/src/bundled-tools.js +21 -0
  33. package/dist/src/bundled-tools.js.map +1 -0
  34. package/dist/src/chat.js +6 -5
  35. package/dist/src/chat.js.map +1 -1
  36. package/dist/src/creation/contracts.d.ts +38 -0
  37. package/dist/src/creation/contracts.js +2 -0
  38. package/dist/src/creation/contracts.js.map +1 -0
  39. package/dist/src/creation/service.d.ts +7 -0
  40. package/dist/src/creation/service.js +196 -0
  41. package/dist/src/creation/service.js.map +1 -0
  42. package/dist/src/index.d.ts +10 -0
  43. package/dist/src/index.js +10 -0
  44. package/dist/src/index.js.map +1 -1
  45. package/dist/src/install/installer.js +32 -10
  46. package/dist/src/install/installer.js.map +1 -1
  47. package/dist/src/orchestration/personas.d.ts +15 -0
  48. package/dist/src/orchestration/personas.js +51 -0
  49. package/dist/src/orchestration/personas.js.map +1 -0
  50. package/dist/src/orchestration/pi-executor.d.ts +1 -0
  51. package/dist/src/orchestration/pi-executor.js +1 -1
  52. package/dist/src/orchestration/pi-executor.js.map +1 -1
  53. package/dist/src/panel/extension.js +29 -8
  54. package/dist/src/panel/extension.js.map +1 -1
  55. package/dist/src/panel/server.js +14 -5
  56. package/dist/src/panel/server.js.map +1 -1
  57. package/dist/src/project/paths.d.ts +3 -0
  58. package/dist/src/project/paths.js +7 -0
  59. package/dist/src/project/paths.js.map +1 -1
  60. package/dist/src/rules/user-rules.d.ts +8 -0
  61. package/dist/src/rules/user-rules.js +36 -0
  62. package/dist/src/rules/user-rules.js.map +1 -0
  63. package/dist/src/skills/contracts.d.ts +4 -4
  64. package/dist/src/skills/recommended.js +1 -1
  65. package/dist/src/skills/registry.js +49 -28
  66. package/dist/src/skills/registry.js.map +1 -1
  67. package/dist/src/style/cli-ui.js +0 -1
  68. package/dist/src/style/cli-ui.js.map +1 -1
  69. package/package.json +14 -3
  70. package/scripts/rebrand-pi.mjs +6 -0
  71. package/skills/recommended/catalog.json +2 -11
  72. package/vendor/ars/.claude/CLAUDE.md +371 -0
  73. package/vendor/ars/.command-invariants.toml +24 -0
  74. package/vendor/ars/CITATION.cff +35 -0
  75. package/vendor/ars/LICENSE +417 -0
  76. package/vendor/ars/MODE_REGISTRY.md +76 -0
  77. package/vendor/ars/NOTICE.md +26 -0
  78. package/vendor/ars/POSITIONING.md +99 -0
  79. package/vendor/ars/PSYCLAW_SOURCE.json +10 -0
  80. package/vendor/ars/README.md +751 -0
  81. package/vendor/ars/SECURITY.md +52 -0
  82. package/vendor/ars/THIRD_PARTY.md +70 -0
  83. package/vendor/ars/academic-paper/SKILL.md +542 -0
  84. package/vendor/ars/academic-paper/agents/abstract_bilingual_agent.md +171 -0
  85. package/vendor/ars/academic-paper/agents/argument_builder_agent.md +276 -0
  86. package/vendor/ars/academic-paper/agents/citation_compliance_agent.md +422 -0
  87. package/vendor/ars/academic-paper/agents/draft_writer_agent.md +656 -0
  88. package/vendor/ars/academic-paper/agents/formatter_agent.md +999 -0
  89. package/vendor/ars/academic-paper/agents/intake_agent.md +393 -0
  90. package/vendor/ars/academic-paper/agents/literature_strategist_agent.md +626 -0
  91. package/vendor/ars/academic-paper/agents/peer_reviewer_agent.md +516 -0
  92. package/vendor/ars/academic-paper/agents/revision_coach_agent.md +334 -0
  93. package/vendor/ars/academic-paper/agents/socratic_mentor_agent.md +527 -0
  94. package/vendor/ars/academic-paper/agents/structure_architect_agent.md +401 -0
  95. package/vendor/ars/academic-paper/agents/visualization_agent.md +441 -0
  96. package/vendor/ars/academic-paper/examples/chinese_paper_example.md +278 -0
  97. package/vendor/ars/academic-paper/examples/clinical_citation_verification_checklist.md +95 -0
  98. package/vendor/ars/academic-paper/examples/clinical_epistemic_status_example.md +100 -0
  99. package/vendor/ars/academic-paper/examples/commitment_ledger_example.md +147 -0
  100. package/vendor/ars/academic-paper/examples/imrad_hei_example.md +234 -0
  101. package/vendor/ars/academic-paper/examples/literature_review_example.md +260 -0
  102. package/vendor/ars/academic-paper/examples/plan_mode_guided_writing.md +600 -0
  103. package/vendor/ars/academic-paper/examples/revision_mode_example.md +344 -0
  104. package/vendor/ars/academic-paper/examples/revision_recovery_example.md +506 -0
  105. package/vendor/ars/academic-paper/examples/version_family_reconciliation_example.md +89 -0
  106. package/vendor/ars/academic-paper/references/abstract_writing_guide.md +169 -0
  107. package/vendor/ars/academic-paper/references/academic_writing_style.md +188 -0
  108. package/vendor/ars/academic-paper/references/anti_leakage_protocol.md +83 -0
  109. package/vendor/ars/academic-paper/references/apa7_chinese_citation_guide.md +364 -0
  110. package/vendor/ars/academic-paper/references/apa7_extended_guide.md +198 -0
  111. package/vendor/ars/academic-paper/references/changelog.md +11 -0
  112. package/vendor/ars/academic-paper/references/citation_format_switcher.md +228 -0
  113. package/vendor/ars/academic-paper/references/committee_correspondence_protocol.md +158 -0
  114. package/vendor/ars/academic-paper/references/credit_authorship_guide.md +308 -0
  115. package/vendor/ars/academic-paper/references/disclosure_mode_protocol.md +478 -0
  116. package/vendor/ars/academic-paper/references/domain_evidence_profiles.md +38 -0
  117. package/vendor/ars/academic-paper/references/failure_paths.md +349 -0
  118. package/vendor/ars/academic-paper/references/funding_statement_guide.md +319 -0
  119. package/vendor/ars/academic-paper/references/hei_domain_glossary.md +169 -0
  120. package/vendor/ars/academic-paper/references/intro_title_rhetoric_guide.md +114 -0
  121. package/vendor/ars/academic-paper/references/journal_submission_guide.md +249 -0
  122. package/vendor/ars/academic-paper/references/latex_template_reference.md +378 -0
  123. package/vendor/ars/academic-paper/references/mode_selection_guide.md +378 -0
  124. package/vendor/ars/academic-paper/references/paper_structure_patterns.md +330 -0
  125. package/vendor/ars/academic-paper/references/plan_mode_protocol.md +112 -0
  126. package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md +200 -0
  127. package/vendor/ars/academic-paper/references/policy_anchor_table.md +157 -0
  128. package/vendor/ars/academic-paper/references/revision_patch_protocol.md +173 -0
  129. package/vendor/ars/academic-paper/references/statistical_visualization_standards.md +750 -0
  130. package/vendor/ars/academic-paper/references/venue_disclosure_policies.md +259 -0
  131. package/vendor/ars/academic-paper/references/vlm_figure_verification.md +126 -0
  132. package/vendor/ars/academic-paper/references/workflow_phase_details.md +135 -0
  133. package/vendor/ars/academic-paper/references/writing_judgment_framework.md +59 -0
  134. package/vendor/ars/academic-paper/references/writing_quality_check.md +173 -0
  135. package/vendor/ars/academic-paper/templates/bilingual_abstract_template.md +78 -0
  136. package/vendor/ars/academic-paper/templates/case_study_template.md +129 -0
  137. package/vendor/ars/academic-paper/templates/conference_paper_template.md +108 -0
  138. package/vendor/ars/academic-paper/templates/credit_statement_template.md +132 -0
  139. package/vendor/ars/academic-paper/templates/funding_statement_template.md +290 -0
  140. package/vendor/ars/academic-paper/templates/imrad_template.md +183 -0
  141. package/vendor/ars/academic-paper/templates/latex_article_template.tex +199 -0
  142. package/vendor/ars/academic-paper/templates/literature_review_template.md +135 -0
  143. package/vendor/ars/academic-paper/templates/policy_brief_template.md +139 -0
  144. package/vendor/ars/academic-paper/templates/revision_tracking_template.md +199 -0
  145. package/vendor/ars/academic-paper/templates/theoretical_paper_template.md +119 -0
  146. package/vendor/ars/academic-paper-reviewer/SKILL.md +491 -0
  147. package/vendor/ars/academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md +443 -0
  148. package/vendor/ars/academic-paper-reviewer/agents/domain_reviewer_agent.md +412 -0
  149. package/vendor/ars/academic-paper-reviewer/agents/editorial_synthesizer_agent.md +478 -0
  150. package/vendor/ars/academic-paper-reviewer/agents/eic_agent.md +339 -0
  151. package/vendor/ars/academic-paper-reviewer/agents/field_analyst_agent.md +221 -0
  152. package/vendor/ars/academic-paper-reviewer/agents/methodology_reviewer_agent.md +449 -0
  153. package/vendor/ars/academic-paper-reviewer/agents/perspective_reviewer_agent.md +427 -0
  154. package/vendor/ars/academic-paper-reviewer/examples/hei_paper_review_example.md +391 -0
  155. package/vendor/ars/academic-paper-reviewer/examples/interdisciplinary_review_example.md +299 -0
  156. package/vendor/ars/academic-paper-reviewer/examples/subclaim_decomposition_example.md +80 -0
  157. package/vendor/ars/academic-paper-reviewer/references/calibration_mode_protocol.md +256 -0
  158. package/vendor/ars/academic-paper-reviewer/references/changelog.md +10 -0
  159. package/vendor/ars/academic-paper-reviewer/references/editorial_decision_standards.md +236 -0
  160. package/vendor/ars/academic-paper-reviewer/references/guided_mode_protocol.md +34 -0
  161. package/vendor/ars/academic-paper-reviewer/references/integration_guide.md +15 -0
  162. package/vendor/ars/academic-paper-reviewer/references/quality_rubrics.md +84 -0
  163. package/vendor/ars/academic-paper-reviewer/references/re_review_mode_protocol.md +340 -0
  164. package/vendor/ars/academic-paper-reviewer/references/review_criteria_framework.md +98 -0
  165. package/vendor/ars/academic-paper-reviewer/references/review_panel_provenance_protocol.md +197 -0
  166. package/vendor/ars/academic-paper-reviewer/references/review_quality_thinking.md +58 -0
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  169. package/vendor/ars/academic-paper-reviewer/references/statistical_reporting_standards.md +505 -0
  170. package/vendor/ars/academic-paper-reviewer/references/top_journals_by_field.md +206 -0
  171. package/vendor/ars/academic-paper-reviewer/templates/editorial_decision_template.md +235 -0
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  175. package/vendor/ars/academic-pipeline/agents/claim_ref_alignment_audit_agent.md +382 -0
  176. package/vendor/ars/academic-pipeline/agents/collaboration_depth_agent.md +164 -0
  177. package/vendor/ars/academic-pipeline/agents/integrity_verification_agent.md +870 -0
  178. package/vendor/ars/academic-pipeline/agents/pipeline_orchestrator_agent.md +1379 -0
  179. package/vendor/ars/academic-pipeline/agents/state_tracker_agent.md +622 -0
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  181. package/vendor/ars/academic-pipeline/examples/integrity_failure_recovery.md +389 -0
  182. package/vendor/ars/academic-pipeline/examples/mid_entry_example.md +414 -0
  183. package/vendor/ars/academic-pipeline/references/adapters/.gitkeep +0 -0
  184. package/vendor/ars/academic-pipeline/references/adapters/overview.md +153 -0
  185. package/vendor/ars/academic-pipeline/references/ai_research_failure_modes.md +185 -0
  186. package/vendor/ars/academic-pipeline/references/changelog.md +14 -0
  187. package/vendor/ars/academic-pipeline/references/claim_audit_calibration_protocol.md +175 -0
  188. package/vendor/ars/academic-pipeline/references/claim_verification_protocol.md +282 -0
  189. package/vendor/ars/academic-pipeline/references/external_review_protocol.md +131 -0
  190. package/vendor/ars/academic-pipeline/references/integrity_review_protocol.md +110 -0
  191. package/vendor/ars/academic-pipeline/references/literature_corpus_consumers.md +193 -0
  192. package/vendor/ars/academic-pipeline/references/mode_advisor.md +135 -0
  193. package/vendor/ars/academic-pipeline/references/passport_as_reset_boundary.md +132 -0
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  204. package/vendor/ars/agents/report_compiler_agent.md +341 -0
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  207. package/vendor/ars/commands/ars-3w.md +10 -0
  208. package/vendor/ars/commands/ars-abstract.md +10 -0
  209. package/vendor/ars/commands/ars-cache-invalidate.md +20 -0
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  213. package/vendor/ars/commands/ars-full.md +9 -0
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  1048. package/vendor/windows/x64/rg.exe +0 -0
@@ -0,0 +1,40 @@
1
+ #!/usr/bin/env python3
2
+ """/ars-cache-invalidate CLI — drop cached verification entries for a citation.
3
+
4
+ Backs the `/ars-cache-invalidate <citation_key>` slash command (Delta 2,
5
+ deliverable 6). Removes every cached resolver entry (all resolvers, all query
6
+ forms) for the named citation_key so the next pipeline run re-verifies it live.
7
+ Idempotent: invalidating a citation with no cached rows succeeds as a no-op.
8
+
9
+ Spec: docs/design/2026-05-21-v3.10-182-promote-citation-gate-spec.md §2 Delta 2.
10
+ """
11
+ from __future__ import annotations
12
+
13
+ import argparse
14
+ import sys
15
+
16
+ try:
17
+ from verification_cache import VerificationCache
18
+ except ImportError:
19
+ from scripts.verification_cache import VerificationCache
20
+
21
+
22
+ def main(argv: list[str] | None = None) -> int:
23
+ parser = argparse.ArgumentParser(
24
+ prog="ars-cache-invalidate",
25
+ description="Drop cached verification entries for a citation_key.",
26
+ )
27
+ parser.add_argument(
28
+ "citation_key",
29
+ help="The citation_key whose cached resolver entries to invalidate.",
30
+ )
31
+ args = parser.parse_args(argv)
32
+
33
+ cache = VerificationCache()
34
+ cache.invalidate(args.citation_key)
35
+ print(f"[ars-cache-invalidate] cleared cache for '{args.citation_key}'")
36
+ return 0
37
+
38
+
39
+ if __name__ == "__main__":
40
+ sys.exit(main())
@@ -0,0 +1,521 @@
1
+ """ARS /ars-mark-read + /ars-unmark-read CLI implementation.
2
+
3
+ Implements v3.6.8 spec §3.6 + Step 7 (round-2 R2-002, round-5 R5-003 amends).
4
+
5
+ The command writes a peer file `<passport-stem>_human_read_log.yaml` next to
6
+ the active passport. The peer file is the canonical user-owned attestation source;
7
+ the literature_corpus[] schema is adapter-owned and MUST NOT be mutated to
8
+ carry reading-attestation state (v3.6.8 §3.1 firm rule 3).
9
+
10
+ Usage:
11
+ python3 scripts/ars_mark_read.py <citation_key>... --passport-path <path> --scope <level>
12
+ python3 scripts/ars_mark_read.py <citation_key>... --passport-path <path> --unmark
13
+
14
+ Behavior summary:
15
+ - 4 fail-fast modes (no passport / not found / parent unreadable / unwritable)
16
+ emit canonical `[ARS-MARK-READ ERROR: ...]` and exit non-zero.
17
+ - Invalid citation_key (not in active corpus) is a hard error per §3.6 firm
18
+ rule 2. Batch with any invalid key is rejected whole (no partial writes).
19
+ - Append-only YAML write per §3.6 firm rule 3. /ars-unmark-read writes
20
+ `rescinded_at` to the matching entry, never deletes.
21
+ - First-time write creates the file with the YAML schema header. Not a
22
+ fail-fast condition.
23
+ - #513/#738 read_scope attestation (declaration-only, never inferred): every
24
+ new mark requires an explicit
25
+ `--scope {full_text,sections,abstract_only,toc_only,unknown}` records HOW
26
+ MUCH of the source was read; `--locator` (repeatable, requires
27
+ `--scope sections`) names the read sections/pages; `--note` free text
28
+ (requires `--scope`). Scope-less records remain valid only as legacy input;
29
+ consumers treat their coverage as unknown and never promote them to `ok`.
30
+ Every new entry is labelled `USER_ATTESTED_READ`: this is the user's
31
+ declaration, not proof of reading or comprehension.
32
+ Attestation args are rejected with `--unmark` (rescinding takes no
33
+ attestation). One invocation's attestation applies to every key in the
34
+ batch. Sidecar schema: shared/contracts/passport/human_read_log.schema.json.
35
+ """
36
+ from __future__ import annotations
37
+
38
+ import argparse
39
+ import errno
40
+ import fcntl
41
+ import os
42
+ import sys
43
+ import tempfile
44
+ import time
45
+ import uuid
46
+ from contextlib import contextmanager
47
+ from datetime import datetime, timezone
48
+ from pathlib import Path
49
+ from typing import Any, Iterator
50
+
51
+ import yaml
52
+
53
+ try:
54
+ from scripts.human_read_attestation_resolver import (
55
+ LedgerValidationError,
56
+ _UniqueKeySafeLoader,
57
+ _validated_rows,
58
+ )
59
+ except ModuleNotFoundError: # direct ``python scripts/ars_mark_read.py`` use
60
+ from human_read_attestation_resolver import ( # type: ignore[no-redef]
61
+ LedgerValidationError,
62
+ _UniqueKeySafeLoader,
63
+ _validated_rows,
64
+ )
65
+
66
+ ERR_PREFIX = "[ARS-MARK-READ ERROR:"
67
+
68
+ # #513 closed level enum + text bounds — keep in lockstep with
69
+ # shared/contracts/passport/human_read_log.schema.json (level enum; locators
70
+ # items minLength 1 / maxLength 200; note minLength 1 / maxLength 1000). The
71
+ # CLI enforces the bounds at write time so it can never produce a ledger the
72
+ # committed schema rejects (codex #513 r1 P1).
73
+ READ_SCOPE_LEVELS = ("full_text", "sections", "abstract_only", "toc_only", "unknown")
74
+ LOCATOR_MAX_LEN = 200
75
+ NOTE_MAX_LEN = 1000
76
+ LEDGER_LOCK_TIMEOUT_SECONDS = 10.0
77
+ LEDGER_LOCK_POLL_SECONDS = 0.05
78
+
79
+
80
+ class LedgerLockError(RuntimeError):
81
+ """The same-directory ledger transaction lock could not be used."""
82
+
83
+
84
+ def _err(msg: str) -> str:
85
+ return f"{ERR_PREFIX} {msg}]"
86
+
87
+
88
+ def _now_iso() -> str:
89
+ return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
90
+
91
+
92
+ def _read_log_path(passport_path: Path) -> Path:
93
+ return passport_path.parent / f"{passport_path.stem}_human_read_log.yaml"
94
+
95
+
96
+ def _ledger_lock_path(log_path: Path) -> Path:
97
+ """Return the stable peer lock path for one ledger.
98
+
99
+ The lock file is deliberately persistent. Unlinking it after release can
100
+ split concurrent writers across different inodes and defeat advisory
101
+ locking even though every writer appears to hold a lock.
102
+ """
103
+ return log_path.parent / f".{log_path.name}.lock"
104
+
105
+
106
+ @contextmanager
107
+ def _ledger_lock(
108
+ log_path: Path,
109
+ *,
110
+ timeout_seconds: float | None = None,
111
+ ) -> Iterator[None]:
112
+ """Acquire a bounded, same-directory exclusive advisory lock.
113
+
114
+ Every read/validate/mutate/replace transaction must run inside this lock.
115
+ Acquisition is non-blocking with a bounded retry loop so contention or an
116
+ unusable lock path fails visibly instead of hanging a command forever.
117
+ """
118
+ timeout = (
119
+ LEDGER_LOCK_TIMEOUT_SECONDS
120
+ if timeout_seconds is None
121
+ else timeout_seconds
122
+ )
123
+ if timeout < 0:
124
+ raise LedgerLockError("ledger lock timeout must be non-negative")
125
+
126
+ lock_path = _ledger_lock_path(log_path)
127
+ flags = os.O_RDWR | os.O_CREAT
128
+ if hasattr(os, "O_CLOEXEC"):
129
+ flags |= os.O_CLOEXEC
130
+ if hasattr(os, "O_NOFOLLOW"):
131
+ flags |= os.O_NOFOLLOW
132
+ try:
133
+ fd = os.open(lock_path, flags, 0o600)
134
+ except OSError as exc:
135
+ raise LedgerLockError(f"cannot open peer lock: {exc}") from exc
136
+
137
+ acquired = False
138
+ try:
139
+ deadline = time.monotonic() + timeout
140
+ while True:
141
+ try:
142
+ fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB)
143
+ acquired = True
144
+ break
145
+ except InterruptedError:
146
+ continue
147
+ except OSError as exc:
148
+ if exc.errno in (errno.EACCES, errno.EAGAIN):
149
+ remaining = deadline - time.monotonic()
150
+ if remaining <= 0:
151
+ raise LedgerLockError(
152
+ f"timed out after {timeout:g}s waiting for peer lock"
153
+ ) from exc
154
+ time.sleep(min(LEDGER_LOCK_POLL_SECONDS, remaining))
155
+ continue
156
+ raise LedgerLockError(
157
+ f"cannot acquire peer lock: {exc}"
158
+ ) from exc
159
+
160
+ yield
161
+ finally:
162
+ active_exception = sys.exc_info()[0] is not None
163
+ release_error: OSError | None = None
164
+ if acquired:
165
+ try:
166
+ fcntl.flock(fd, fcntl.LOCK_UN)
167
+ except OSError as exc:
168
+ release_error = exc
169
+ try:
170
+ os.close(fd)
171
+ except OSError as exc:
172
+ if release_error is None:
173
+ release_error = exc
174
+ if release_error is not None and not active_exception:
175
+ raise LedgerLockError(
176
+ f"cannot release peer lock cleanly: {release_error}"
177
+ ) from release_error
178
+
179
+
180
+ def _validate_passport_environment(passport_path: Path | None) -> tuple[Path, Path]:
181
+ """Run the 4 fail-fast checks per §3.6 R5-003 amend.
182
+
183
+ Returns (passport_path, read_log_path) if all checks pass; raises
184
+ SystemExit with the canonical error message otherwise.
185
+ """
186
+ if passport_path is None:
187
+ print(
188
+ _err(
189
+ "no active passport path; run a session with passport "
190
+ "handoff first or pass --passport-path explicitly"
191
+ ),
192
+ file=sys.stderr,
193
+ )
194
+ raise SystemExit(2)
195
+
196
+ parent = passport_path.parent
197
+ # Check parent R_OK BEFORE passport.exists() — pathlib's stat() raises
198
+ # PermissionError on an unreadable parent, which would mask the canonical
199
+ # error we want to emit.
200
+ if not os.access(parent, os.R_OK):
201
+ print(
202
+ _err(f"passport parent directory {parent} unreadable"),
203
+ file=sys.stderr,
204
+ )
205
+ raise SystemExit(2)
206
+
207
+ if not passport_path.exists():
208
+ print(_err(f"passport file not found at {passport_path}"), file=sys.stderr)
209
+ raise SystemExit(2)
210
+
211
+ if not os.access(parent, os.W_OK):
212
+ log_path = _read_log_path(passport_path)
213
+ print(
214
+ _err(
215
+ f"read-log path target is unwritable at {log_path}; "
216
+ "parent directory not writable"
217
+ ),
218
+ file=sys.stderr,
219
+ )
220
+ raise SystemExit(2)
221
+
222
+ log_path = _read_log_path(passport_path)
223
+ if log_path.exists() and not os.access(log_path, os.W_OK):
224
+ print(
225
+ _err(
226
+ f"read-log path target is unwritable at {log_path}; "
227
+ "existing file not writable"
228
+ ),
229
+ file=sys.stderr,
230
+ )
231
+ raise SystemExit(2)
232
+
233
+ return passport_path, log_path
234
+
235
+
236
+ def _load_corpus_keys(passport_path: Path) -> set[str]:
237
+ with passport_path.open(encoding="utf-8") as f:
238
+ passport = yaml.safe_load(f) or {}
239
+ corpus = passport.get("literature_corpus", []) or []
240
+ return {entry["citation_key"] for entry in corpus if "citation_key" in entry}
241
+
242
+
243
+ def _load_log(log_path: Path) -> dict[str, Any]:
244
+ """Load an existing ledger only after duplicate-safe closed validation.
245
+
246
+ Mutation commands are intentionally stricter than PyYAML's default
247
+ loader: duplicate mapping keys, malformed UTF-8/YAML, missing fields,
248
+ unknown fields, invalid timestamps, and invalid row/scope combinations
249
+ all fail closed. In particular, this function never repairs or defaults
250
+ an existing ledger because doing so would destroy the evidence needed to
251
+ diagnose it.
252
+ """
253
+ if not log_path.exists():
254
+ return {
255
+ "session_id": str(uuid.uuid4()),
256
+ "created_at": _now_iso(),
257
+ "human_read": [],
258
+ }
259
+
260
+ try:
261
+ raw = log_path.read_bytes()
262
+ text = raw.decode("utf-8")
263
+ except (OSError, UnicodeDecodeError) as exc:
264
+ raise LedgerValidationError(
265
+ f"existing ledger cannot be read as UTF-8: {exc}"
266
+ ) from exc
267
+ try:
268
+ data = yaml.load(text, Loader=_UniqueKeySafeLoader)
269
+ except yaml.YAMLError as exc:
270
+ raise LedgerValidationError(
271
+ f"existing ledger is not duplicate-safe valid YAML: {exc}"
272
+ ) from exc
273
+
274
+ # This is the same closed runtime contract used by the resolver. Calling
275
+ # it here, before returning the object to main(), guarantees there is no
276
+ # mutation path from an invalid on-disk ledger.
277
+ _validated_rows(data)
278
+ return data
279
+
280
+
281
+ def _save_log(log_path: Path, data: dict[str, Any]) -> None:
282
+ """Validate and atomically replace the ledger from a same-dir temp file.
283
+
284
+ The destination is never opened with ``"w"``. A serialization, flush,
285
+ fsync, or replace failure therefore leaves an existing ledger untouched;
286
+ an owned temporary file is removed on failure.
287
+ """
288
+ _validated_rows(data)
289
+ payload = yaml.safe_dump(
290
+ data, sort_keys=False, allow_unicode=True
291
+ ).encode("utf-8")
292
+ temp_path: Path | None = None
293
+ try:
294
+ with tempfile.NamedTemporaryFile(
295
+ mode="wb",
296
+ dir=log_path.parent,
297
+ prefix=f".{log_path.name}.",
298
+ suffix=".tmp",
299
+ delete=False,
300
+ ) as temp_file:
301
+ temp_path = Path(temp_file.name)
302
+ temp_file.write(payload)
303
+ temp_file.flush()
304
+ os.fsync(temp_file.fileno())
305
+ os.replace(temp_path, log_path)
306
+ temp_path = None
307
+ finally:
308
+ if temp_path is not None:
309
+ try:
310
+ temp_path.unlink()
311
+ except FileNotFoundError:
312
+ pass
313
+
314
+
315
+ def _mark(log: dict, citation_key: str, read_scope: dict | None = None) -> None:
316
+ entry: dict = {
317
+ "citation_key": citation_key,
318
+ "marked_at": _now_iso(),
319
+ "attestation_type": "USER_ATTESTED_READ",
320
+ }
321
+ if read_scope is not None:
322
+ entry["read_scope"] = read_scope
323
+ log["human_read"].append(entry)
324
+
325
+
326
+ def _build_read_scope(args: argparse.Namespace) -> dict | None:
327
+ """Validate the #513 attestation flags and build the read_scope object.
328
+
329
+ Returns None only for unmark, the read_scope dict when a new mark is
330
+ valid, or raises SystemExit(2) with the canonical
331
+ error surface on a contradictory attestation — a contradictory or
332
+ partial attestation is refused, never recorded ambiguously."""
333
+ # Presence is `is not None`, NEVER truthiness: `--note ""` is an explicitly
334
+ # supplied (invalid) attestation argument, not an absent one — truthiness
335
+ # would let it bypass both the requires-scope rule and the unmark rejection
336
+ # (codex #513 r1 P1).
337
+ locator_given = args.locator is not None
338
+ note_given = args.note is not None
339
+ errors: list[str] = []
340
+ if args.unmark and (args.scope is not None or locator_given or note_given):
341
+ errors.append("--scope/--locator/--note cannot be combined with --unmark (rescinding takes no attestation)")
342
+ elif args.scope is None:
343
+ if not args.unmark:
344
+ errors.append(
345
+ "--scope is required for every new USER_ATTESTED_READ mark; "
346
+ "use --scope unknown when coverage cannot be specified"
347
+ )
348
+ if locator_given:
349
+ errors.append("--locator requires --scope sections (an attestation needs a declared level)")
350
+ if note_given:
351
+ errors.append("--note requires --scope (an attestation needs a declared level)")
352
+ else:
353
+ if locator_given and args.scope != "sections":
354
+ errors.append(
355
+ f"--locator requires --scope sections; with --scope {args.scope} "
356
+ "locators are redundant or contradict the declared level"
357
+ )
358
+ if locator_given:
359
+ for loc in args.locator:
360
+ if not 1 <= len(loc) <= LOCATOR_MAX_LEN:
361
+ errors.append(
362
+ f"--locator value must be 1-{LOCATOR_MAX_LEN} characters "
363
+ f"(got {len(loc)}); the sidecar schema would reject the ledger"
364
+ )
365
+ if note_given and not 1 <= len(args.note) <= NOTE_MAX_LEN:
366
+ errors.append(
367
+ f"--note must be 1-{NOTE_MAX_LEN} characters (got {len(args.note)}); "
368
+ "the sidecar schema would reject the ledger"
369
+ )
370
+ if errors:
371
+ for e in errors:
372
+ print(_err(e), file=sys.stderr)
373
+ raise SystemExit(2)
374
+ if args.scope is None:
375
+ return None
376
+ read_scope: dict = {"level": args.scope}
377
+ if locator_given:
378
+ read_scope["locators"] = list(args.locator)
379
+ if note_given:
380
+ read_scope["note"] = args.note
381
+ return read_scope
382
+
383
+
384
+ def _unmark(log: dict, citation_key: str) -> bool:
385
+ """Append `rescinded_at` to the most recent matching entry without a
386
+ prior rescind. Returns True if found, False otherwise."""
387
+ for entry in reversed(log["human_read"]):
388
+ if entry["citation_key"] == citation_key and "rescinded_at" not in entry:
389
+ entry["rescinded_at"] = _now_iso()
390
+ return True
391
+ return False
392
+
393
+
394
+ def _update_log_locked(
395
+ log_path: Path,
396
+ citation_keys: list[str],
397
+ *,
398
+ read_scope: dict | None,
399
+ unmark: bool,
400
+ ) -> list[str]:
401
+ """Reload, validate, mutate, and atomically replace under one lock.
402
+
403
+ Returning missing active marks keeps batch unmark all-or-nothing: the
404
+ in-memory partial mutation is discarded and no replacement occurs.
405
+ """
406
+ with _ledger_lock(log_path):
407
+ log = _load_log(log_path)
408
+ if unmark:
409
+ not_found = [
410
+ key for key in citation_keys if not _unmark(log, key)
411
+ ]
412
+ if not_found:
413
+ return not_found
414
+ else:
415
+ for key in citation_keys:
416
+ _mark(log, key, read_scope)
417
+ _save_log(log_path, log)
418
+ return []
419
+
420
+
421
+ def main(argv: list[str] | None = None) -> int:
422
+ parser = argparse.ArgumentParser(
423
+ description="ARS /ars-mark-read peer-file writer (v3.6.8 §3.6)."
424
+ )
425
+ parser.add_argument(
426
+ "citation_keys",
427
+ nargs="+",
428
+ help="Citation keys to mark (or unmark with --unmark).",
429
+ )
430
+ parser.add_argument(
431
+ "--passport-path",
432
+ type=Path,
433
+ default=None,
434
+ help="Active Material Passport JSON path.",
435
+ )
436
+ parser.add_argument(
437
+ "--unmark",
438
+ action="store_true",
439
+ help="Rescind prior marks (write rescinded_at instead of marked_at).",
440
+ )
441
+ parser.add_argument(
442
+ "--scope",
443
+ choices=READ_SCOPE_LEVELS,
444
+ default=None,
445
+ help="#513/#738 USER_ATTESTED_READ scope: how much of the source the "
446
+ "user declares reading. Required for new marks; use unknown when "
447
+ "coverage cannot be specified.",
448
+ )
449
+ parser.add_argument(
450
+ "--locator",
451
+ action="append",
452
+ default=None,
453
+ help="Which sections/pages were read (repeatable; requires --scope sections).",
454
+ )
455
+ parser.add_argument(
456
+ "--note",
457
+ default=None,
458
+ help="Free-text attestation note (requires --scope).",
459
+ )
460
+ args = parser.parse_args(argv)
461
+
462
+ passport_path, log_path = _validate_passport_environment(args.passport_path)
463
+ corpus_keys = _load_corpus_keys(passport_path)
464
+
465
+ # Validate all keys up-front; refuse to write on any invalid key
466
+ # (§3.6 firm rule 2, batch-level all-or-nothing).
467
+ invalid = [k for k in args.citation_keys if k not in corpus_keys]
468
+ if invalid:
469
+ for k in invalid:
470
+ print(
471
+ _err(f"citation_key '{k}' not in literature_corpus[]"),
472
+ file=sys.stderr,
473
+ )
474
+ return 2
475
+
476
+ # Preserve the four canonical environment errors and corpus-membership
477
+ # error before enforcing the new-mark attestation shape.
478
+ read_scope = _build_read_scope(args)
479
+
480
+ try:
481
+ not_found = _update_log_locked(
482
+ log_path,
483
+ args.citation_keys,
484
+ read_scope=read_scope,
485
+ unmark=args.unmark,
486
+ )
487
+ except LedgerLockError as exc:
488
+ print(
489
+ _err(
490
+ "read ledger lock lifecycle failed; mutation status is not "
491
+ f"assumed: {exc}"
492
+ ),
493
+ file=sys.stderr,
494
+ )
495
+ return 2
496
+ except LedgerValidationError as exc:
497
+ print(
498
+ _err(f"existing read ledger is invalid; refusing mutation: {exc}"),
499
+ file=sys.stderr,
500
+ )
501
+ return 2
502
+ except (OSError, yaml.YAMLError) as exc:
503
+ print(
504
+ _err(f"read ledger write failed without in-place truncation: {exc}"),
505
+ file=sys.stderr,
506
+ )
507
+ return 2
508
+ if not_found:
509
+ for k in not_found:
510
+ print(
511
+ _err(
512
+ f"citation_key '{k}' has no active mark to rescind"
513
+ ),
514
+ file=sys.stderr,
515
+ )
516
+ return 2
517
+ return 0
518
+
519
+
520
+ if __name__ == "__main__":
521
+ sys.exit(main())
@@ -0,0 +1,33 @@
1
+ {
2
+ "version": 1,
3
+ "spec": "docs/design/2026-06-01-ars-134-conductor-rescope-deterministic-write-guard-spec.md",
4
+ "source": "docs/design/2026-05-18-ars-v3.9.2-agent-phase-classification.md",
5
+ "_about": "Machine-readable write-scope manifest for the 23 Bucket A agents (22 single-phase + draft_writer_agent, which carries a documented dual-phase static union — see `_known_multiphase_static_union`). Consumed by the PreToolUse write-scope guard (hooks/ars_write_scope_guard.py) to deny out-of-scope structured-tool writes. Keys are agent frontmatter `name` values (NOT filenames). `allowed_write_globs` is the AUTHORITATIVE scope expression (workspace-root-anchored, matched against the hook's normalized relative path); `phase` is a human-readable label cross-referencing the classification table only (it is skill-relative, not global, so a phase integer is not globally meaningful). Each glob mirrors the agent's own Phase Boundary prompt rule: an agent may write only into its own `phase<N>_*/` directory. The named outputs a few agents emit (see `known_named_outputs`) all live under that same own-phase directory, so the phase-dir glob already permits them; the field is documentation only and is NOT a second enforcement channel (no `**/<file>` anywhere-globs, which would WIDEN scope past the phase dir — a precision regression, not a gain).",
6
+ "_coverage_claim": "Deterministic for the structured editing tools (Write/Edit/MultiEdit); ALL Bash is denied for a Bucket A agent (it uses the Grep/Glob tools to search and the structured tools to write), so no Bash write path remains for a fenced agent (see spec section 3.3 + the Implementation-outcome note: neither a denylist nor an allowlist of Bash is decidable from a command string, so all-deny is the only zero-fail-open policy). This guard is sound for single-skill runs and for the #133 failure shape (an agent writing into a DIFFERENT phase number than its own). It does NOT disambiguate same-phase-number cross-skill collisions (e.g. academic-paper-reviewer Phase 1 vs deep-research Phase 1 both glob `phase1_*/`) in a hypothetical shared flat workspace — that lower-probability risk is deferred until the full-pipeline workspace layout is first-party confirmed (spec section 7 open item). It also enforces phase ISOLATION, not artifact OWNERSHIP: an agent may still overwrite another file inside its own phase dir. Stated explicitly per no-silent-caps discipline.",
7
+ "_known_multiphase_static_union": "draft_writer_agent is the ONLY Bucket A entry whose `allowed_write_globs` is a multi-phase static union (`phase4_*/**` + `phase6_*/**`) rather than a single own-phase glob. This is a KNOWN, BOUNDED Slice-1 limitation tracked at issue #330, not an oversight. Why the phase6 leg is load-bearing: draft_writer genuinely operates at Phase 4 (initial drafting) OR Phase 6 (revision-after-review) depending on the caller invocation — both its own `## Phase Boundary` block and the #390 patch-document revision path (which writes `phase6_*/revision_patch_round<N>.json` via the Write tool) exercise the phase6 leg. The PreToolUse payload carries only `agent_type`, never the invocation phase, so the guard cannot distinguish a Phase 4 draft call from a Phase 6 revision call from a single manifest key; a static union of the two phase globs is the only single-key expression that keeps BOTH legitimate write paths open. The cost (stated, not silently capped): a Phase 4 invocation is permitted to write `phase6_*/` and vice-versa — inflation bounded to this one agent and the phase4<->phase6 pair. This weakens draft_writer's Bucket A fence in the same way the spec uses to justify EXEMPTING the Bucket B multi-phase agents (report_compiler_agent shares draft_writer's Phase 4,6 signature but is Bucket B). The DISPOSITION (narrow to `phase4_*/**` now and route phase6 writes elsewhere / reclassify alongside Bucket B / keep the union) is DEFERRED to #330, to be decided when Slice 3 is scoped — the real fix is per-invocation scope grants from the dispatching layer (spec §5 item 3), at which point the static union is no longer needed. Documented here so the limitation is visible at the enforcement surface, not to settle the decision.",
8
+ "agents": {
9
+ "research_question_agent": { "bucket": "A", "skill": "deep-research", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
10
+ "research_architect_agent": { "bucket": "A", "skill": "deep-research", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
11
+ "bibliography_agent": { "bucket": "A", "skill": "deep-research", "phase": "2", "allowed_write_globs": ["phase2_*/**"], "known_named_outputs": ["phase2_*/pre_screened_citation_keys_*.txt"] },
12
+ "source_verification_agent": { "bucket": "A", "skill": "deep-research", "phase": "2", "allowed_write_globs": ["phase2_*/**"] },
13
+ "timeline_extraction_agent": { "bucket": "A", "skill": "deep-research", "phase": "2", "allowed_write_globs": ["phase2_*/**"], "known_named_outputs": ["phase2_investigation/timeline.yaml", "phase2_investigation/citation_provenance.yaml", "phase2_investigation/version_records.yaml"] },
14
+ "synthesis_agent": { "bucket": "A", "skill": "deep-research", "phase": "3", "allowed_write_globs": ["phase3_*/**"] },
15
+ "editor_in_chief_agent": { "bucket": "A", "skill": "deep-research", "phase": "5", "allowed_write_globs": ["phase5_*/**"] },
16
+ "ethics_review_agent": { "bucket": "A", "skill": "deep-research", "phase": "5", "allowed_write_globs": ["phase5_*/**"] },
17
+ "risk_of_bias_agent": { "bucket": "A", "skill": "deep-research", "phase": "SR2", "allowed_write_globs": ["phase2_*/**"] },
18
+ "meta_analysis_agent": { "bucket": "A", "skill": "deep-research", "phase": "SR3", "allowed_write_globs": ["phase3_*/**"] },
19
+ "literature_strategist_agent": { "bucket": "A", "skill": "academic-paper", "phase": "1", "allowed_write_globs": ["phase1_*/**"], "known_named_outputs": ["phase1_*/pre_screened_citation_keys_*.txt"] },
20
+ "structure_architect_agent": { "bucket": "A", "skill": "academic-paper", "phase": "2", "allowed_write_globs": ["phase2_*/**"] },
21
+ "draft_writer_agent": { "bucket": "A", "skill": "academic-paper", "phase": "4", "allowed_write_globs": ["phase4_*/**", "phase6_*/**"], "_note": "Dual-phase static union (phase4 drafting | phase6 revision, per invocation) — the one Bucket A multi-phase entry. Known bounded inflation, tracked #330; disposition deferred to Slice 3 per-invocation grants. See top-level `_known_multiphase_static_union`." },
22
+ "citation_compliance_agent": { "bucket": "A", "skill": "academic-paper", "phase": "5a", "allowed_write_globs": ["phase5_*/**"] },
23
+ "abstract_bilingual_agent": { "bucket": "A", "skill": "academic-paper", "phase": "5b", "allowed_write_globs": ["phase5_*/**"] },
24
+ "peer_reviewer_agent": { "bucket": "A", "skill": "academic-paper", "phase": "6", "allowed_write_globs": ["phase6_*/**"] },
25
+ "formatter_agent": { "bucket": "A", "skill": "academic-paper", "phase": "7", "allowed_write_globs": ["phase7_*/**"], "known_named_outputs": ["phase7_*/paper.md", "phase7_*/paper.tex", "phase7_*/references.bib", "phase7_*/cover_letter.md", "phase7_*/provenance_summary.md"] },
26
+ "eic_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
27
+ "methodology_reviewer_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
28
+ "domain_reviewer_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
29
+ "perspective_reviewer_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
30
+ "devils_advocate_reviewer_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "1", "allowed_write_globs": ["phase1_*/**"] },
31
+ "editorial_synthesizer_agent": { "bucket": "A", "skill": "academic-paper-reviewer", "phase": "2", "allowed_write_globs": ["phase2_*/**"] }
32
+ }
33
+ }