mednotes-opencode 0.1.0

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Files changed (430) hide show
  1. package/.opencode/agents/med-chat-triager.md +204 -0
  2. package/.opencode/agents/med-flashcard-maker.md +63 -0
  3. package/.opencode/agents/med-knowledge-architect.md +230 -0
  4. package/.opencode/agents/med-link-graph-curator.md +177 -0
  5. package/.opencode/agents/med-publish-guard.md +62 -0
  6. package/.opencode/commands/flashcards.md +25 -0
  7. package/.opencode/commands/mednotes/create.md +25 -0
  8. package/.opencode/commands/mednotes/enrich.md +27 -0
  9. package/.opencode/commands/mednotes/fix-wiki.md +27 -0
  10. package/.opencode/commands/mednotes/history.md +22 -0
  11. package/.opencode/commands/mednotes/link-body.md +25 -0
  12. package/.opencode/commands/mednotes/link-related.md +27 -0
  13. package/.opencode/commands/mednotes/link.md +27 -0
  14. package/.opencode/commands/mednotes/pdf-library.md +27 -0
  15. package/.opencode/commands/mednotes/process-chats.md +23 -0
  16. package/.opencode/commands/mednotes/setup.md +21 -0
  17. package/.opencode/commands/mednotes/status.md +27 -0
  18. package/.opencode/commands/mednotes/telemetry.md +27 -0
  19. package/.opencode/commands/report.md +26 -0
  20. package/.opencode/mednotes/AGENTS.md +57 -0
  21. package/.opencode/mednotes/agents/med-chat-triager.md +197 -0
  22. package/.opencode/mednotes/agents/med-flashcard-maker.md +56 -0
  23. package/.opencode/mednotes/agents/med-knowledge-architect.md +224 -0
  24. package/.opencode/mednotes/agents/med-link-graph-curator.md +171 -0
  25. package/.opencode/mednotes/agents/med-publish-guard.md +55 -0
  26. package/.opencode/mednotes/contracts/.gitkeep +1 -0
  27. package/.opencode/mednotes/contracts/agents.json +116 -0
  28. package/.opencode/mednotes/contracts/opencode-plugin.json +70 -0
  29. package/.opencode/mednotes/docs/agent-prompt-hardening.md +567 -0
  30. package/.opencode/mednotes/docs/agent-role-contracts.md +94 -0
  31. package/.opencode/mednotes/docs/anki-mcp-twenty-rules.md +214 -0
  32. package/.opencode/mednotes/docs/anki-templates/README.md +39 -0
  33. package/.opencode/mednotes/docs/anki-templates/cloze.back.html +23 -0
  34. package/.opencode/mednotes/docs/anki-templates/cloze.front.html +14 -0
  35. package/.opencode/mednotes/docs/anki-templates/qa.back.html +24 -0
  36. package/.opencode/mednotes/docs/anki-templates/qa.front.html +14 -0
  37. package/.opencode/mednotes/docs/anki-templates/style.css +182 -0
  38. package/.opencode/mednotes/docs/atomicity-splitting-policy.md +113 -0
  39. package/.opencode/mednotes/docs/extension-docs.md +40 -0
  40. package/.opencode/mednotes/docs/flashcard-ingestion.md +278 -0
  41. package/.opencode/mednotes/docs/knowledge-architect.md +208 -0
  42. package/.opencode/mednotes/docs/merge-policy.md +110 -0
  43. package/.opencode/mednotes/docs/public-vocabulary.md +104 -0
  44. package/.opencode/mednotes/docs/semantic-linker.md +141 -0
  45. package/.opencode/mednotes/docs/taxonomy-policy.md +90 -0
  46. package/.opencode/mednotes/docs/triage-policy.md +187 -0
  47. package/.opencode/mednotes/docs/vault-version-control.md +758 -0
  48. package/.opencode/mednotes/docs/vocabulary-db-recovery.md +58 -0
  49. package/.opencode/mednotes/docs/workflow-output-contract.md +779 -0
  50. package/.opencode/mednotes/hooks/hooks.json +79 -0
  51. package/.opencode/mednotes/package-lock.json +6361 -0
  52. package/.opencode/mednotes/package.json +15 -0
  53. package/.opencode/mednotes/pyproject.toml +48 -0
  54. package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.cmd +13 -0
  55. package/.opencode/mednotes/scripts/bootstrap_windows_python_uv.ps1 +172 -0
  56. package/.opencode/mednotes/scripts/enrich_notes.py +23 -0
  57. package/.opencode/mednotes/scripts/full_reset_windows_python_uv.cmd +13 -0
  58. package/.opencode/mednotes/scripts/hooks/antigravity_hook_status.mjs +212 -0
  59. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/antigravity.mjs +169 -0
  60. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/harness_payload.mjs +103 -0
  61. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_plugin.mjs +341 -0
  62. package/.opencode/mednotes/scripts/hooks/mednotes_hook/adapters/opencode_user_config_sync.mjs +177 -0
  63. package/.opencode/mednotes/scripts/hooks/mednotes_hook/anki_preflight.mjs +214 -0
  64. package/.opencode/mednotes/scripts/hooks/mednotes_hook/cli.mjs +143 -0
  65. package/.opencode/mednotes/scripts/hooks/mednotes_hook/diagnostics.mjs +11 -0
  66. package/.opencode/mednotes/scripts/hooks/mednotes_hook/domain/agent_directive_core.mjs +160 -0
  67. package/.opencode/mednotes/scripts/hooks/mednotes_hook/fsm_directive.mjs +1470 -0
  68. package/.opencode/mednotes/scripts/hooks/mednotes_hook/hook_errors.mjs +120 -0
  69. package/.opencode/mednotes/scripts/hooks/mednotes_hook/retention.mjs +114 -0
  70. package/.opencode/mednotes/scripts/hooks/mednotes_hook/runtime.mjs +174 -0
  71. package/.opencode/mednotes/scripts/hooks/mednotes_hook/telemetry_capture.mjs +511 -0
  72. package/.opencode/mednotes/scripts/hooks/mednotes_hook/vault_guard.mjs +624 -0
  73. package/.opencode/mednotes/scripts/hooks/mednotes_hook.mjs +5 -0
  74. package/.opencode/mednotes/scripts/mednotes/_runtime_paths.py +24 -0
  75. package/.opencode/mednotes/scripts/mednotes/anki_model_validator.py +18 -0
  76. package/.opencode/mednotes/scripts/mednotes/capture_extension_diff.py +1562 -0
  77. package/.opencode/mednotes/scripts/mednotes/feedback_report.py +16 -0
  78. package/.opencode/mednotes/scripts/mednotes/flashcard_index.py +18 -0
  79. package/.opencode/mednotes/scripts/mednotes/flashcard_pipeline.py +18 -0
  80. package/.opencode/mednotes/scripts/mednotes/flashcard_report.py +18 -0
  81. package/.opencode/mednotes/scripts/mednotes/flashcard_sources.py +18 -0
  82. package/.opencode/mednotes/scripts/mednotes/obsidian/README.md +6 -0
  83. package/.opencode/mednotes/scripts/mednotes/obsidian_note_utils.py +20 -0
  84. package/.opencode/mednotes/scripts/mednotes/pdf_library/cli.py +16 -0
  85. package/.opencode/mednotes/scripts/mednotes/project_fsm.py +229 -0
  86. package/.opencode/mednotes/scripts/mednotes/setup_telemetry_email.py +404 -0
  87. package/.opencode/mednotes/scripts/mednotes/sync_anki_twenty_rules.py +18 -0
  88. package/.opencode/mednotes/scripts/mednotes/sync_opencode_user_config.py +36 -0
  89. package/.opencode/mednotes/scripts/mednotes/wiki/cli.py +20 -0
  90. package/.opencode/mednotes/scripts/mednotes/wiki_graph.py +18 -0
  91. package/.opencode/mednotes/scripts/mednotes/wiki_tree.py +134 -0
  92. package/.opencode/mednotes/scripts/reset_windows_python_uv.ps1 +625 -0
  93. package/.opencode/mednotes/scripts/run_python.mjs +109 -0
  94. package/.opencode/mednotes/scripts/vault/vault_commit.ps1 +19 -0
  95. package/.opencode/mednotes/scripts/vault/vault_commit.sh +18 -0
  96. package/.opencode/mednotes/scripts/vault/vault_git.ps1 +19 -0
  97. package/.opencode/mednotes/scripts/vault/vault_git.py +3107 -0
  98. package/.opencode/mednotes/scripts/vault/vault_git.sh +18 -0
  99. package/.opencode/mednotes/scripts/vault/vault_precommit.ps1 +19 -0
  100. package/.opencode/mednotes/scripts/vault/vault_precommit.sh +18 -0
  101. package/.opencode/mednotes/skills/THIRD_PARTY_NOTICES.md +45 -0
  102. package/.opencode/mednotes/skills/create-medical-flashcards/SKILL.md +113 -0
  103. package/.opencode/mednotes/skills/create-medical-note/SKILL.md +90 -0
  104. package/.opencode/mednotes/skills/enrich-medical-note/SKILL.md +120 -0
  105. package/.opencode/mednotes/skills/fix-medical-wiki/SKILL.md +559 -0
  106. package/.opencode/mednotes/skills/link-medical-wiki/SKILL.md +224 -0
  107. package/.opencode/mednotes/skills/obsidian-cli/SKILL.md +118 -0
  108. package/.opencode/mednotes/skills/obsidian-markdown/SKILL.md +207 -0
  109. package/.opencode/mednotes/skills/obsidian-markdown/references/CALLOUTS.md +58 -0
  110. package/.opencode/mednotes/skills/obsidian-markdown/references/EMBEDS.md +63 -0
  111. package/.opencode/mednotes/skills/obsidian-markdown/references/PROPERTIES.md +61 -0
  112. package/.opencode/mednotes/skills/obsidian-ops/SKILL.md +136 -0
  113. package/.opencode/mednotes/skills/pdf-library/SKILL.md +45 -0
  114. package/.opencode/mednotes/skills/process-medical-chats/SKILL.md +246 -0
  115. package/.opencode/mednotes/skills/workflow-report/SKILL.md +100 -0
  116. package/.opencode/mednotes/src/mednotes/__init__.py +5 -0
  117. package/.opencode/mednotes/src/mednotes/domains/__init__.py +5 -0
  118. package/.opencode/mednotes/src/mednotes/domains/flashcards/README.md +26 -0
  119. package/.opencode/mednotes/src/mednotes/domains/flashcards/__init__.py +2 -0
  120. package/.opencode/mednotes/src/mednotes/domains/flashcards/build_demo_apkg.py +177 -0
  121. package/.opencode/mednotes/src/mednotes/domains/flashcards/contracts.py +385 -0
  122. package/.opencode/mednotes/src/mednotes/domains/flashcards/flashcards_machine.py +522 -0
  123. package/.opencode/mednotes/src/mednotes/domains/flashcards/fsm.py +817 -0
  124. package/.opencode/mednotes/src/mednotes/domains/flashcards/index.py +630 -0
  125. package/.opencode/mednotes/src/mednotes/domains/flashcards/install_models.py +445 -0
  126. package/.opencode/mednotes/src/mednotes/domains/flashcards/model.py +359 -0
  127. package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_links.py +135 -0
  128. package/.opencode/mednotes/src/mednotes/domains/flashcards/obsidian_note_utils.py +546 -0
  129. package/.opencode/mednotes/src/mednotes/domains/flashcards/pipeline.py +580 -0
  130. package/.opencode/mednotes/src/mednotes/domains/flashcards/report.py +510 -0
  131. package/.opencode/mednotes/src/mednotes/domains/flashcards/sources.py +682 -0
  132. package/.opencode/mednotes/src/mednotes/domains/flashcards/sync_rules.py +184 -0
  133. package/.opencode/mednotes/src/mednotes/domains/history/__init__.py +1 -0
  134. package/.opencode/mednotes/src/mednotes/domains/history/history_fsm.py +852 -0
  135. package/.opencode/mednotes/src/mednotes/domains/history/history_machine.py +453 -0
  136. package/.opencode/mednotes/src/mednotes/domains/setup/__init__.py +7 -0
  137. package/.opencode/mednotes/src/mednotes/domains/setup/setup_fsm.py +808 -0
  138. package/.opencode/mednotes/src/mednotes/domains/setup/setup_machine.py +973 -0
  139. package/.opencode/mednotes/src/mednotes/domains/wiki/README.md +64 -0
  140. package/.opencode/mednotes/src/mednotes/domains/wiki/__init__.py +1 -0
  141. package/.opencode/mednotes/src/mednotes/domains/wiki/api.py +668 -0
  142. package/.opencode/mednotes/src/mednotes/domains/wiki/batch_state.py +102 -0
  143. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/__init__.py +1 -0
  144. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/__init__.py +1 -0
  145. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/atomicity/atomicity.py +877 -0
  146. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/__init__.py +1 -0
  147. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/body_link/body_linker.py +1562 -0
  148. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/__init__.py +1 -0
  149. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/effect_adapters.py +949 -0
  150. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/effects/fix_wiki_runtime_adapters.py +433 -0
  151. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/__init__.py +1 -0
  152. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/coverage.py +413 -0
  153. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph.py +396 -0
  154. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/graph/graph_fixes.py +161 -0
  155. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/__init__.py +1 -0
  156. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/hygiene/hygiene.py +483 -0
  157. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/__init__.py +2 -0
  158. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/anchors.py +185 -0
  159. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/__init__.py +0 -0
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  161. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/config.py +131 -0
  162. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/download.py +224 -0
  163. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/frontmatter.py +59 -0
  164. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/insert.py +227 -0
  165. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/core/local_import.py +54 -0
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  167. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_profiles.py +99 -0
  168. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/web_search.py +203 -0
  169. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/illustrate/sources/wikimedia.py +102 -0
  170. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/__init__.py +1 -0
  171. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_db_adapter.mjs +434 -0
  172. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_node_runtime.py +274 -0
  173. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/markdown/markdown_query.py +227 -0
  174. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/__init__.py +1 -0
  175. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/artifacts.py +605 -0
  176. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/canonical_merge.py +277 -0
  177. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/markdown_zones.py +85 -0
  178. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/meaning_planner.py +307 -0
  179. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_iter.py +67 -0
  180. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_merge.py +278 -0
  181. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_plan.py +409 -0
  182. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_policy.py +22 -0
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  186. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/models.py +208 -0
  187. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/prompts.py +37 -0
  188. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/tables.py +236 -0
  189. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/note_style/validate.py +404 -0
  190. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/provenance.py +478 -0
  191. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/raw_chats.py +273 -0
  192. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/notes/sources_backfill.py +235 -0
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  195. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/pdf/captions.py +47 -0
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  239. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/subagents/agents.py +1767 -0
  240. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/__init__.py +1 -0
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  243. package/.opencode/mednotes/src/mednotes/domains/wiki/capabilities/vocabulary/llm_disambiguation.py +182 -0
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  430. package/package.json +45 -0
@@ -0,0 +1,103 @@
1
+ export function firstString(...values) {
2
+ for (const value of values) {
3
+ if (typeof value === "string" && value.length > 0) return value;
4
+ if (typeof value === "number" && Number.isFinite(value)) return String(value);
5
+ }
6
+ return "";
7
+ }
8
+
9
+ export function firstObject(...values) {
10
+ for (const value of values) {
11
+ if (value && typeof value === "object" && !Array.isArray(value)) return value;
12
+ }
13
+ return {};
14
+ }
15
+
16
+ export function normalizedArgs(args) {
17
+ const input = args && typeof args === "object" ? { ...args } : {};
18
+ const command = firstString(input.command, input.cmd, input.script, input.CommandLine);
19
+ const cwd = firstString(input.cwd, input.Cwd, input.workingDirectory, input.WorkingDirectory);
20
+ const target = firstString(
21
+ input.file_path,
22
+ input.filePath,
23
+ input.path,
24
+ input.TargetFile,
25
+ input.AbsolutePath,
26
+ input.SearchDirectory,
27
+ input.DirectoryPath,
28
+ );
29
+ if (command) input.command = command;
30
+ if (cwd) input.cwd = cwd;
31
+ if (target) {
32
+ input.file_path = target;
33
+ input.target_file = target;
34
+ }
35
+ return input;
36
+ }
37
+
38
+ export function isAgyRuntime(payload) {
39
+ return (
40
+ Boolean(payload?.antigravity_payload_seen) ||
41
+ Boolean(payload?.hookEventName || payload?.conversationId || payload?.workspacePaths)
42
+ );
43
+ }
44
+
45
+ export function runtimeFromPayload(payload) {
46
+ if (isAgyRuntime(payload)) return "antigravity";
47
+ if (
48
+ payload?.opencode_payload_seen ||
49
+ payload?.opencodePayloadSeen ||
50
+ String(payload?.runtime || "").toLowerCase() === "opencode" ||
51
+ String(payload?.harness || "").toLowerCase() === "opencode"
52
+ ) {
53
+ return "opencode";
54
+ }
55
+ return "gemini-cli";
56
+ }
57
+
58
+ export function isOpenCodeRuntime(payload, card = null) {
59
+ return runtimeFromPayload(payload) === "opencode" || String(card?.runtime || "") === "opencode";
60
+ }
61
+
62
+ export function sessionIdFromPayload(payload) {
63
+ return cleanFileStem(String(payload?.session_id || payload?.conversation_id || payload?.conversationId || ""));
64
+ }
65
+
66
+ export function cleanFileStem(value) {
67
+ return String(value || "")
68
+ .replace(/[^a-zA-Z0-9_.-]/g, "_")
69
+ .slice(0, 120);
70
+ }
71
+
72
+ export function toolInput(payload) {
73
+ return firstObject(payload?.tool_input, payload?.toolInput, payload?.input, payload?.parameters, payload?.args);
74
+ }
75
+
76
+ export function normalizedToolName(payload) {
77
+ return String(payload?.tool_name || payload?.toolName || payload?.name || payload?.tool || "")
78
+ .trim()
79
+ .toLowerCase();
80
+ }
81
+
82
+ export function toolCommandLine(payload) {
83
+ const input = toolInput(payload);
84
+ return String(input.command || input.CommandLine || input.commandLine || input.cmd || input.script || "");
85
+ }
86
+
87
+ export function hookEventNameFromPayload(payload) {
88
+ return String(payload?.hook_event_name || payload?.hookEventName || "");
89
+ }
90
+
91
+ export function normalizeHookEvent(payload, card = null) {
92
+ const runtime = card && String(card.runtime || "") ? String(card.runtime) : runtimeFromPayload(payload);
93
+ return {
94
+ runtime,
95
+ eventName: hookEventNameFromPayload(payload),
96
+ sessionId: sessionIdFromPayload(payload),
97
+ toolName: normalizedToolName(payload),
98
+ toolInput: toolInput(payload),
99
+ toolResponse: firstObject(payload?.tool_response, payload?.toolResponse, payload?.response, payload?.result),
100
+ cwd: String(payload?.cwd || ""),
101
+ transcriptPath: String(payload?.transcript_path || payload?.transcriptPath || ""),
102
+ };
103
+ }
@@ -0,0 +1,341 @@
1
+ import crypto from "node:crypto";
2
+ import fs from "node:fs/promises";
3
+ import os from "node:os";
4
+ import path from "node:path";
5
+
6
+ import {
7
+ captureAgentDirectiveAfterTool,
8
+ guardAgentDirectiveBeforeTool,
9
+ injectAgentDirectiveBeforeAgent,
10
+ } from "../fsm_directive.mjs";
11
+ import { applyMedNotesOpenCodeRuntimeConfig } from "./opencode_user_config_sync.mjs";
12
+
13
+ const OPENCODE_TASK_METADATA_SCHEMA = "medical-notes-workbench.opencode-specialist-task-metadata.v1";
14
+ const OPENCODE_SPECIALIST_RAW_CONTENT_KEYS = new Set([
15
+ "content",
16
+ "markdown",
17
+ "raw_chat",
18
+ "raw_chat_content",
19
+ "raw_markdown",
20
+ "raw_markdown_content",
21
+ "note_text",
22
+ "html",
23
+ ]);
24
+ const OPENCODE_SPECIALIST_SAFE_TEXT_KEYS = new Set([
25
+ "agent",
26
+ "attestation_created_by",
27
+ "expected_model",
28
+ "item_type",
29
+ "model_policy",
30
+ "missing_specialist_task_run_receipt_action",
31
+ "phase",
32
+ "preferred_model_tier",
33
+ "raw_file",
34
+ "required_model_tier",
35
+ "rewrite_prompt",
36
+ "schema",
37
+ "source_work_id",
38
+ "specialist_task_run_receipt_path",
39
+ "staged_title",
40
+ "target_hash_before",
41
+ "target_path",
42
+ "target_kind",
43
+ "temp_output",
44
+ "temp_output_path",
45
+ "title",
46
+ "coverage_path",
47
+ "taxonomy",
48
+ "work_id",
49
+ "write_markdown_to",
50
+ "write_policy",
51
+ ]);
52
+
53
+ function hookPayload(input, output = {}, eventName) {
54
+ const toolState = firstObjectValue(output?.state, input?.state, output?.part?.state, input?.part?.state);
55
+ return {
56
+ hook_event_name: eventName,
57
+ runtime: "opencode",
58
+ opencode_payload_seen: true,
59
+ session_id: String(input?.sessionID || ""),
60
+ tool_name: opencodeToolName(input, output),
61
+ tool_input: firstObjectValue(output?.args, input?.args, toolState.input, output?.input, input?.input),
62
+ tool_response: {
63
+ title: String(output?.title || toolState.title || ""),
64
+ output: String(output?.output || toolState.output || ""),
65
+ metadata: firstObjectValue(output?.metadata, input?.metadata, toolState.metadata),
66
+ },
67
+ };
68
+ }
69
+
70
+ function opencodeToolName(input, output = {}) {
71
+ return String(
72
+ input?.tool || output?.tool || input?.toolName || output?.toolName || input?.part?.tool || output?.part?.tool || "",
73
+ ).toLowerCase();
74
+ }
75
+
76
+ function denialMessage(result) {
77
+ if (result?.decision !== "deny") return "";
78
+ return [result.blocked_reason, result.directive_field, result.reason, result.agent_message]
79
+ .filter(Boolean)
80
+ .join(" | ");
81
+ }
82
+
83
+ function appHomeDir() {
84
+ return path.resolve(process.env.MEDNOTES_HOME || path.join(os.homedir(), ".mednotes"));
85
+ }
86
+
87
+ function safeFileStem(value) {
88
+ return (
89
+ String(value || "")
90
+ .replace(/[^a-zA-Z0-9_.-]/g, "_")
91
+ .slice(0, 120) || "unknown"
92
+ );
93
+ }
94
+
95
+ function objectValue(value) {
96
+ return value && typeof value === "object" && !Array.isArray(value) ? value : {};
97
+ }
98
+
99
+ function firstObjectValue(...values) {
100
+ for (const value of values) {
101
+ const candidate = objectValue(value);
102
+ if (Object.keys(candidate).length > 0) return candidate;
103
+ }
104
+ return {};
105
+ }
106
+
107
+ function sha256Text(value) {
108
+ return `sha256:${crypto
109
+ .createHash("sha256")
110
+ .update(String(value || ""))
111
+ .digest("hex")}`;
112
+ }
113
+
114
+ function parseJsonObjectFromText(value) {
115
+ const text = String(value || "").trim();
116
+ try {
117
+ const parsed = JSON.parse(text);
118
+ return parsed && typeof parsed === "object" && !Array.isArray(parsed) ? parsed : {};
119
+ } catch {
120
+ // Continue below for prompts that wrap the JSON work item with small prose.
121
+ }
122
+ const start = text.indexOf("{");
123
+ if (start < 0) return {};
124
+ let depth = 0;
125
+ let inString = false;
126
+ let escaped = false;
127
+ for (let index = start; index < text.length; index += 1) {
128
+ const char = text[index];
129
+ if (escaped) {
130
+ escaped = false;
131
+ continue;
132
+ }
133
+ if (char === "\\") {
134
+ escaped = true;
135
+ continue;
136
+ }
137
+ if (char === '"') {
138
+ inString = !inString;
139
+ continue;
140
+ }
141
+ if (inString) continue;
142
+ if (char === "{") depth += 1;
143
+ if (char === "}") {
144
+ depth -= 1;
145
+ if (depth === 0) {
146
+ try {
147
+ const parsed = JSON.parse(text.slice(start, index + 1));
148
+ return parsed && typeof parsed === "object" && !Array.isArray(parsed) ? parsed : {};
149
+ } catch {
150
+ return {};
151
+ }
152
+ }
153
+ }
154
+ }
155
+ return {};
156
+ }
157
+
158
+ function typedWorkItemFromPrompt(prompt) {
159
+ const packet = parseJsonObjectFromText(prompt);
160
+ const candidates = [
161
+ packet,
162
+ objectValue(packet.work_item),
163
+ objectValue(packet.workItem),
164
+ ...(Array.isArray(packet.current_batch_items) ? packet.current_batch_items : []),
165
+ ...(Array.isArray(packet.currentBatchItems) ? packet.currentBatchItems : []),
166
+ ];
167
+ for (const candidate of candidates) {
168
+ const workItem = objectValue(candidate);
169
+ if (!workItem.work_id || !workItem.temp_output) continue;
170
+ if (isStyleRewriteWorkItem(workItem) || isArchitectWorkItem(workItem)) return workItem;
171
+ }
172
+ return {};
173
+ }
174
+
175
+ function isStyleRewriteWorkItem(workItem) {
176
+ if (!workItem.target_hash_before) return false;
177
+ if (!workItem.subagent_output_contract || typeof workItem.subagent_output_contract !== "object") return false;
178
+ return true;
179
+ }
180
+
181
+ function isArchitectWorkItem(workItem) {
182
+ const expected = objectValue(workItem.expected_output_schema);
183
+ if (String(workItem.phase || "") !== "architect") return false;
184
+ if (String(workItem.agent || "") !== "med-knowledge-architect") return false;
185
+ if (String(workItem.item_type || "") !== "meaning_work_item") return false;
186
+ if (String(expected.schema || "") !== "medical-notes-workbench.architect-output.v1") return false;
187
+ if (!workItem.raw_file) return false;
188
+ return true;
189
+ }
190
+
191
+ function architectOutputFromTaskResponse(outputText) {
192
+ const payload = parseJsonObjectFromText(outputText);
193
+ if (String(payload.schema || "") !== "medical-notes-workbench.architect-output.v1") {
194
+ return {};
195
+ }
196
+ return payload;
197
+ }
198
+
199
+ async function writeArchitectOutputArtifact(workItem, outputText) {
200
+ if (!isArchitectWorkItem(workItem)) return;
201
+ const artifact = architectOutputFromTaskResponse(outputText);
202
+ if (!artifact.schema) return;
203
+ if (String(artifact.temp_output_path || "") !== String(workItem.temp_output || "")) return;
204
+ const baseDir = path.join(appHomeDir(), "hook-state", "opencode-task-output");
205
+ const byWorkIdPath = path.join(baseDir, "by-work-id", `${safeFileStem(workItem.work_id)}.json`);
206
+ const text = `${JSON.stringify(artifact, null, 2)}\n`;
207
+ await fs.mkdir(path.dirname(byWorkIdPath), { recursive: true });
208
+ await fs.writeFile(byWorkIdPath, text, "utf8");
209
+ }
210
+
211
+ function looksLikeRawContent(prompt) {
212
+ const text = String(prompt || "");
213
+ return (
214
+ /(^|\n)---\s*\n[\s\S]{0,200}\n---\s*\n#\s+/m.test(text) ||
215
+ /\bChats_Raw\b|\bWiki_Medicina\b|\[Chat Original\]|gemini\.google\.com\/app\//i.test(text) ||
216
+ /<(?:!doctype|html|body|article|section)\b/i.test(text)
217
+ );
218
+ }
219
+
220
+ function promptEmbedsRawContent(prompt) {
221
+ const packet = parseJsonObjectFromText(prompt);
222
+ const items = Array.isArray(packet.current_batch_items) ? packet.current_batch_items : [];
223
+ if (items.length === 1 && Object.keys(packet).length === 1) {
224
+ return workItemEmbedsRawContent(items[0]);
225
+ }
226
+ return looksLikeRawContent(prompt);
227
+ }
228
+
229
+ function workItemEmbedsRawContent(value, parentKey = "") {
230
+ if (Array.isArray(value)) return value.some((item) => workItemEmbedsRawContent(item, parentKey));
231
+ if (!value || typeof value !== "object") {
232
+ if (typeof value !== "string") return false;
233
+ const key = String(parentKey || "").toLowerCase();
234
+ if (OPENCODE_SPECIALIST_SAFE_TEXT_KEYS.has(key)) return false;
235
+ return looksLikeRawContent(value);
236
+ }
237
+ for (const [key, item] of Object.entries(value)) {
238
+ const normalizedKey = String(key || "").toLowerCase();
239
+ if (OPENCODE_SPECIALIST_RAW_CONTENT_KEYS.has(normalizedKey)) return true;
240
+ if (workItemEmbedsRawContent(item, normalizedKey)) return true;
241
+ }
242
+ return false;
243
+ }
244
+
245
+ async function writeNativeTaskMetadata(input, output = {}) {
246
+ const toolName = String(input?.tool || output?.tool || input?.part?.tool || output?.part?.tool || "").toLowerCase();
247
+ if (toolName !== "task") return;
248
+ const state = firstObjectValue(output?.state, input?.state, output?.part?.state, input?.part?.state);
249
+ const status = String(state.status || output?.status || input?.status || "").toLowerCase();
250
+ if (status && status !== "completed") return;
251
+ const args = firstObjectValue(output?.args, input?.args, state.input, output?.input, input?.input);
252
+ const prompt = String(args?.prompt || "");
253
+ const workItem = typedWorkItemFromPrompt(prompt);
254
+ if (!workItem.work_id) return;
255
+ const metadata = firstObjectValue(
256
+ output?.metadata,
257
+ input?.metadata,
258
+ state.metadata,
259
+ output?.part?.state?.metadata,
260
+ input?.part?.state?.metadata,
261
+ );
262
+ const model = objectValue(metadata.model);
263
+ const taskSessionId = String(metadata.sessionId || "");
264
+ const parentSessionId = String(metadata.parentSessionId || input?.sessionID || "");
265
+ const providerId = String(model.providerID || "");
266
+ const modelId = String(model.modelID || "");
267
+ if (!taskSessionId || !parentSessionId || !providerId || !modelId) return;
268
+
269
+ const payload = {
270
+ schema: OPENCODE_TASK_METADATA_SCHEMA,
271
+ work_id: String(workItem.work_id),
272
+ task_id: taskSessionId,
273
+ parent_session_id: parentSessionId,
274
+ specialist_session_id: taskSessionId,
275
+ provider_id: providerId,
276
+ model_id: modelId,
277
+ model_tier: "specialist",
278
+ tool_sequence: ["task"],
279
+ prompt_contract: "single_current_batch_items_json",
280
+ raw_content_embedded: promptEmbedsRawContent(prompt),
281
+ capture_source: "opencode_tool_execute_after",
282
+ capture_session_id: String(input?.sessionID || parentSessionId),
283
+ tool_call_id: String(
284
+ input?.callID ||
285
+ input?.callId ||
286
+ output?.callID ||
287
+ output?.callId ||
288
+ input?.part?.callID ||
289
+ output?.part?.callID ||
290
+ "",
291
+ ),
292
+ tool_prompt_sha256: sha256Text(prompt),
293
+ tool_response_sha256: sha256Text(output?.output || state.output || input?.output || ""),
294
+ captured_at: new Date().toISOString(),
295
+ };
296
+ const baseDir = path.join(appHomeDir(), "hook-state", "opencode-task-metadata");
297
+ const byWorkIdPath = path.join(baseDir, "by-work-id", `${safeFileStem(workItem.work_id)}.json`);
298
+ const bySessionPath = path.join(
299
+ baseDir,
300
+ "by-session",
301
+ safeFileStem(parentSessionId),
302
+ `${safeFileStem(workItem.work_id)}.json`,
303
+ );
304
+ const text = `${JSON.stringify(payload, null, 2)}\n`;
305
+ await fs.mkdir(path.dirname(byWorkIdPath), { recursive: true });
306
+ await fs.writeFile(byWorkIdPath, text, "utf8");
307
+ await fs.mkdir(path.dirname(bySessionPath), { recursive: true });
308
+ await fs.writeFile(bySessionPath, text, "utf8");
309
+ await writeArchitectOutputArtifact(workItem, String(output?.output || state.output || input?.output || ""));
310
+ }
311
+
312
+ export const server = async () => ({
313
+ config: async (config) => {
314
+ applyMedNotesOpenCodeRuntimeConfig(config);
315
+ },
316
+ "experimental.chat.system.transform": async (input, output) => {
317
+ const result = await injectAgentDirectiveBeforeAgent({
318
+ hook_event_name: "BeforeAgent",
319
+ runtime: "opencode",
320
+ opencode_payload_seen: true,
321
+ session_id: String(input?.sessionID || ""),
322
+ });
323
+ const context = result?.hookSpecificOutput?.additionalContext;
324
+ if (context) output.system.push(context);
325
+ },
326
+ "tool.execute.before": async (input, output) => {
327
+ const result = await guardAgentDirectiveBeforeTool(hookPayload(input, output, "PreToolUse"));
328
+ const message = denialMessage(result);
329
+ if (message) throw new Error(`mednotes_fsm_hook_blocked: ${message}`);
330
+ },
331
+ "tool.execute.after": async (input, output) => {
332
+ await writeNativeTaskMetadata(input, output);
333
+ await captureAgentDirectiveAfterTool(hookPayload(input, output, "AfterTool"));
334
+ },
335
+ });
336
+
337
+ export const MedNotesFSM = server;
338
+ MedNotesFSM.id = "medical-notes-workbench-fsm";
339
+ MedNotesFSM.server = server;
340
+
341
+ export default MedNotesFSM;
@@ -0,0 +1,177 @@
1
+ import { existsSync, readFileSync, writeFileSync } from "node:fs";
2
+ import os from "node:os";
3
+ import path from "node:path";
4
+ import { fileURLToPath } from "node:url";
5
+
6
+ // OpenCode imports the project plugin before user agents are invoked. This
7
+ // adapter uses that boot point to apply only runtime knobs from the user TOML:
8
+ // specialist model ids and reasoning effort. FSM state and workflow policy do
9
+ // not live here.
10
+ const FIELD_TO_AGENT = new Map([
11
+ ["med_chat_triager", "med-chat-triager"],
12
+ ["med_flashcard_maker", "med-flashcard-maker"],
13
+ ["med_knowledge_architect", "med-knowledge-architect"],
14
+ ["med_link_graph_curator", "med-link-graph-curator"],
15
+ ["med_publish_guard", "med-publish-guard"],
16
+ ]);
17
+ const REASONING_EFFORTS = new Set(["minimal", "low", "medium", "high"]);
18
+
19
+ export function syncMedNotesOpenCodeUserConfig(projectRoot = opencodeProjectRoot()) {
20
+ if (autoSyncDisabled()) return { status: "disabled", agents: [] };
21
+ const runtimeByAgent = readRuntimeOverrides(projectRoot);
22
+ applyRuntimeOverridesToFiles(projectRoot, runtimeByAgent);
23
+ return {
24
+ status: "synced",
25
+ project_root: projectRoot,
26
+ agents: Object.keys(runtimeByAgent).sort(),
27
+ };
28
+ }
29
+
30
+ export function applyMedNotesOpenCodeRuntimeConfig(config, projectRoot = opencodeProjectRoot()) {
31
+ const runtimeByAgent = readRuntimeOverrides(projectRoot);
32
+ config.agent = config.agent && typeof config.agent === "object" ? config.agent : {};
33
+ for (const [agentId, runtimeConfig] of Object.entries(runtimeByAgent)) {
34
+ const entry = config.agent[agentId] && typeof config.agent[agentId] === "object" ? config.agent[agentId] : {};
35
+ config.agent[agentId] = { ...entry, ...runtimeConfig };
36
+ }
37
+ }
38
+
39
+ function readRuntimeOverrides(projectRoot) {
40
+ const configPath = findConfigPath(projectRoot);
41
+ if (!configPath || !existsSync(configPath)) return {};
42
+ return parseAgentRuntimeConfig(readFileSync(configPath, "utf8"), configPath);
43
+ }
44
+
45
+ function applyRuntimeOverridesToFiles(projectRoot, runtimeByAgent) {
46
+ if (Object.keys(runtimeByAgent).length === 0) return;
47
+ updateOpenCodeJson(path.join(projectRoot, ".opencode", "opencode.json"), runtimeByAgent);
48
+ for (const [agentId, runtimeConfig] of Object.entries(runtimeByAgent)) {
49
+ updateAgentMarkdown(path.join(projectRoot, ".opencode", "agents", `${agentId}.md`), runtimeConfig);
50
+ }
51
+ }
52
+
53
+ function updateOpenCodeJson(configPath, runtimeByAgent) {
54
+ if (!existsSync(configPath)) return;
55
+ const parsed = JSON.parse(readFileSync(configPath, "utf8"));
56
+ parsed.agent = parsed.agent && typeof parsed.agent === "object" ? parsed.agent : {};
57
+ for (const [agentId, runtimeConfig] of Object.entries(runtimeByAgent)) {
58
+ const entry = parsed.agent[agentId] && typeof parsed.agent[agentId] === "object" ? parsed.agent[agentId] : {};
59
+ parsed.agent[agentId] = { ...entry, ...runtimeConfig };
60
+ }
61
+ writeIfChanged(configPath, `${JSON.stringify(parsed, null, 2)}\n`);
62
+ }
63
+
64
+ function updateAgentMarkdown(agentPath, runtimeConfig) {
65
+ if (!existsSync(agentPath)) return;
66
+ let text = readFileSync(agentPath, "utf8");
67
+ if (runtimeConfig.model) {
68
+ text = replaceFrontmatterLine(agentPath, text, "model", runtimeConfig.model);
69
+ }
70
+ if (runtimeConfig.reasoningEffort) {
71
+ text = replaceFrontmatterLine(agentPath, text, "reasoningEffort", runtimeConfig.reasoningEffort);
72
+ }
73
+ writeIfChanged(agentPath, text);
74
+ }
75
+
76
+ function replaceFrontmatterLine(agentPath, text, key, value) {
77
+ const pattern = new RegExp(`^${key}: .+$`, "m");
78
+ if (!pattern.test(text)) {
79
+ throw new Error(`MedNotes OpenCode auto-sync could not find ${key} in ${agentPath}`);
80
+ }
81
+ return text.replace(pattern, `${key}: ${frontmatterScalar(value)}`);
82
+ }
83
+
84
+ function parseAgentRuntimeConfig(text, configPath) {
85
+ // The MedNotes config template emits simple [agents.<name>] TOML sections.
86
+ // Keeping this parser narrow avoids making plugin startup depend on Python or
87
+ // a package install before OpenCode opens.
88
+ const runtimeByAgent = {};
89
+ let currentAgentId = "";
90
+ for (const rawLine of text.split(/\r?\n/)) {
91
+ const line = rawLine.trim();
92
+ if (!line || line.startsWith("#")) continue;
93
+
94
+ const section = line.match(/^\[agents\.([A-Za-z0-9_]+)\]$/);
95
+ if (section) {
96
+ currentAgentId = FIELD_TO_AGENT.get(section[1]) || "";
97
+ continue;
98
+ }
99
+ if (line.startsWith("[")) {
100
+ currentAgentId = "";
101
+ continue;
102
+ }
103
+ if (!currentAgentId) continue;
104
+
105
+ const assignment = line.match(/^([A-Za-z0-9_]+)\s*=\s*(.+)$/);
106
+ if (!assignment) continue;
107
+ const key = assignment[1];
108
+ const value = parseTomlStringValue(assignment[2], configPath);
109
+ if (key === "model") {
110
+ if (!value) throw new Error(`MedNotes OpenCode config has empty model for ${currentAgentId}`);
111
+ runtimeByAgent[currentAgentId] = { ...(runtimeByAgent[currentAgentId] || {}), model: value };
112
+ }
113
+ if (key === "reasoning_effort") {
114
+ if (!REASONING_EFFORTS.has(value)) {
115
+ throw new Error(`MedNotes OpenCode config has invalid reasoning_effort for ${currentAgentId}: ${value}`);
116
+ }
117
+ runtimeByAgent[currentAgentId] = { ...(runtimeByAgent[currentAgentId] || {}), reasoningEffort: value };
118
+ }
119
+ }
120
+ return runtimeByAgent;
121
+ }
122
+
123
+ function parseTomlStringValue(rawValue, configPath) {
124
+ const value = rawValue.trim();
125
+ if (value.startsWith('"')) {
126
+ let escaped = false;
127
+ for (let index = 1; index < value.length; index += 1) {
128
+ const char = value[index];
129
+ if (escaped) {
130
+ escaped = false;
131
+ continue;
132
+ }
133
+ if (char === "\\") {
134
+ escaped = true;
135
+ continue;
136
+ }
137
+ if (char === '"') return JSON.parse(value.slice(0, index + 1));
138
+ }
139
+ throw new Error(`Invalid quoted TOML string in ${configPath}`);
140
+ }
141
+ if (value.startsWith("'")) {
142
+ const end = value.indexOf("'", 1);
143
+ if (end > 0) return value.slice(1, end);
144
+ throw new Error(`Invalid literal TOML string in ${configPath}`);
145
+ }
146
+ return value.split("#", 1)[0].trim();
147
+ }
148
+
149
+ function findConfigPath(projectRoot) {
150
+ if (process.env.MEDNOTES_CONFIG) return path.resolve(process.env.MEDNOTES_CONFIG);
151
+ if (process.env.MEDNOTES_HOME) return path.resolve(process.env.MEDNOTES_HOME, "config.toml");
152
+ for (let current = path.resolve(projectRoot); ; current = path.dirname(current)) {
153
+ const candidate = path.join(current, "config.toml");
154
+ if (existsSync(candidate)) return candidate;
155
+ if (current === path.dirname(current)) break;
156
+ }
157
+ return path.join(os.homedir(), ".mednotes", "config.toml");
158
+ }
159
+
160
+ function opencodeProjectRoot() {
161
+ const adapterDir = path.dirname(fileURLToPath(import.meta.url));
162
+ return path.resolve(adapterDir, "..", "..", "..", "..");
163
+ }
164
+
165
+ function autoSyncDisabled() {
166
+ return /^(0|false|no)$/i.test(process.env.MEDNOTES_OPENCODE_AUTO_SYNC || "");
167
+ }
168
+
169
+ function frontmatterScalar(value) {
170
+ const text = String(value);
171
+ return /^[A-Za-z0-9_./:@-]+$/.test(text) ? text : JSON.stringify(text);
172
+ }
173
+
174
+ function writeIfChanged(filePath, nextText) {
175
+ const current = existsSync(filePath) ? readFileSync(filePath, "utf8") : "";
176
+ if (current !== nextText) writeFileSync(filePath, nextText, "utf8");
177
+ }