atris 3.2.0 → 3.11.0

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 (55) hide show
  1. package/GETTING_STARTED.md +65 -131
  2. package/README.md +18 -2
  3. package/atris/GETTING_STARTED.md +65 -131
  4. package/atris/PERSONA.md +5 -1
  5. package/atris/atris.md +122 -153
  6. package/atris/skills/aeo/SKILL.md +117 -0
  7. package/atris/skills/atris/SKILL.md +49 -25
  8. package/atris/skills/create-member/SKILL.md +29 -9
  9. package/atris/skills/endgame/SKILL.md +9 -0
  10. package/atris/skills/research-search/SKILL.md +167 -0
  11. package/atris/skills/research-search/arxiv_search.py +157 -0
  12. package/atris/skills/research-search/program.md +48 -0
  13. package/atris/skills/research-search/results.tsv +6 -0
  14. package/atris/skills/research-search/scholar_search.py +154 -0
  15. package/atris/skills/tidy/SKILL.md +36 -21
  16. package/atris/team/_template/MEMBER.md +2 -0
  17. package/atris/team/validator/MEMBER.md +35 -1
  18. package/atris.md +118 -178
  19. package/bin/atris.js +46 -12
  20. package/cli/__pycache__/atris_code.cpython-314.pyc +0 -0
  21. package/cli/__pycache__/runtime_guard.cpython-312.pyc +0 -0
  22. package/cli/__pycache__/runtime_guard.cpython-314.pyc +0 -0
  23. package/cli/atris_code.py +889 -0
  24. package/cli/runtime_guard.py +693 -0
  25. package/commands/align.js +16 -0
  26. package/commands/app.js +316 -0
  27. package/commands/autopilot.js +863 -23
  28. package/commands/brainstorm.js +7 -5
  29. package/commands/business.js +677 -2
  30. package/commands/clean.js +19 -3
  31. package/commands/computer.js +2022 -43
  32. package/commands/context-sync.js +5 -0
  33. package/commands/integrations.js +14 -9
  34. package/commands/lifecycle.js +12 -0
  35. package/commands/plugin.js +24 -0
  36. package/commands/pull.js +86 -11
  37. package/commands/push.js +153 -9
  38. package/commands/serve.js +1 -0
  39. package/commands/sync.js +272 -76
  40. package/commands/verify.js +50 -1
  41. package/commands/wiki.js +27 -2
  42. package/commands/workflow.js +24 -9
  43. package/lib/file-ops.js +13 -1
  44. package/lib/journal.js +23 -0
  45. package/lib/manifest.js +3 -0
  46. package/lib/scorecard.js +42 -4
  47. package/lib/sync-telemetry.js +59 -0
  48. package/lib/todo.js +6 -0
  49. package/lib/wiki.js +150 -6
  50. package/lib/workspace-safety.js +87 -0
  51. package/package.json +2 -1
  52. package/utils/api.js +19 -0
  53. package/utils/auth.js +25 -1
  54. package/utils/config.js +24 -0
  55. package/utils/update-check.js +16 -0
package/commands/clean.js CHANGED
@@ -197,6 +197,15 @@ function healBrokenMapRefs(cwd, atrisDir, dryRun = false) {
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  // Required delimiter [(,[,—,-] prevents bleeding into adjacent refs on same line
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  const refPattern = /(`?)([a-zA-Z0-9_\-./\\]+\.(js|ts|py|go|rs|rb|java|c|cpp|h|hpp|md|json|yaml|yml)):(\d+)(?:-(\d+))?(`?)([^\S\n]*[\(\[—\-][^\S\n]*([^)\]\n]+))?/g;
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+ // Function Inventory form: `symbolName()` → `file:line[-line]`
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+ // Pre-scan to build a (file:line) → symbol map so refs with the symbol BEFORE them still verify.
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+ const preRefSymbols = {};
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+ const preRefPattern = /`([a-zA-Z_][a-zA-Z0-9_]*)\s*\(?\s*\)?`\s*(?:→|->)\s*`([a-zA-Z0-9_\-./\\]+\.(?:js|ts|py|go|rs|rb|java|c|cpp|h|hpp|md|json|yaml|yml)):(\d+)(?:-\d+)?`/g;
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+ let preMatch;
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+ while ((preMatch = preRefPattern.exec(mapContent)) !== null) {
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+ preRefSymbols[`${preMatch[2]}:${preMatch[3]}`] = preMatch[1];
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+ }
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+
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  // Cache file reads
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  const fileCache = {};
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  function readFileCached(filePath) {
@@ -228,7 +237,8 @@ function healBrokenMapRefs(cwd, atrisDir, dryRun = false) {
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  continue;
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  }
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- const symbol = extractSymbol(contextPart);
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+ let symbol = extractSymbol(contextPart);
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+ if (!symbol) symbol = preRefSymbols[`${filePath}:${startLine}`] || null;
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  // Check if reference is still accurate
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  const outOfBounds = startLine > file.lines.length || (endLine && endLine > file.lines.length);
@@ -445,9 +455,15 @@ function checkPageStaleness(cwd, filePath) {
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  .map(line => line.replace(/^\s+-\s+/, '').trim())
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  .filter(Boolean);
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- // Check each source's mtime against last_compiled
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+ // Check each source's mtime against last_compiled.
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+ // Source entries can include a line range and/or a parenthesized annotation,
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+ // e.g. "bin/atris.js:199-340 (showHelp function)" — strip both before stat.
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  for (const source of sources) {
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- const sourcePath = path.isAbsolute(source) ? source : path.join(cwd, source);
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+ const filePart = source
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+ .replace(/\s*\([^)]*\)\s*$/, '') // drop trailing "(annotation)"
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+ .replace(/:\d+(-\d+)?$/, '') // drop trailing ":N" or ":N-M"
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+ .trim();
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+ const sourcePath = path.isAbsolute(filePart) ? filePart : path.join(cwd, filePart);
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  try {
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  const stat = fs.statSync(sourcePath);
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  if (stat.mtime > compiledDate) {