docs: file verified parse_prd cwd-relative-state + paid-Perplexity drift bugs

Author: claude

ISSUES.md

@@ -0,0 +1,31 @@
+# Known issues
+
+## 2026-07-12 — parse_prd unusable when server cwd ≠ project root; provider drift to paid Perplexity
+Verified by source read (this session, atlas-vault fleet run).
+
+### A. parse_prd `[Errno 2] ... '.atlas-ai'` (Severity: HIGH)
+- `.atlas-ai` state paths are CWD-relative module constants: economy.py:32, fleet.py:17,76,
+  pipeline.py:13-19, feedback.py:10, suggestions.py:20, reputation.py:39-40, task_state.py:401,
+  mcp-server/server.py:394. No stateful op takes a project root.
+- The long-lived atlas-engine MCP server frequently runs with a DELETED cwd (a removed git
+  worktree) → `Path('.atlas-ai').mkdir(...)` at lib.py:88 raises Errno 2 even though the parent
+  mkdir exists. Reached via economy.py telemetry (economy.py:115) from NativeBackend.parse_prd
+  (backend.py:351); error swallowed at mcp-server/server.py:221-222. preflight() also does
+  os.chdir (pipeline.py:192), permanently moving the shared server off-root.
+- Telemetry writes AFTER the LLM call, so the failure burns paid tokens then discards the parse.
+- validate vs parse inconsistency: validation.py:39-41 resolves a relative prd_path against the
+  server cwd (rejects a path valid from project root); parse reads abs fine (backend.py:359-363)
+  but then fails on the cwd-relative WRITE.
+- FIX: anchor all state to an explicit project root (tool param / ATLAS_PROJECT_ROOT env / MCP
+  roots); detect a dead cwd per call and fail self-diagnosing; make append_telemetry best-effort;
+  replace preflight os.chdir with a plumbed root; echo the resolved absolute prd_path in errors.
+
+### B. Research role silently uses paid Perplexity (Severity: MEDIUM)
+- providers.py:352-358: research_choice "real_api_if_key" + has_perplexity_key →
+  _perplexity_research_model("sonar"), which writes NO baseURL → TaskMaster defaults to paid
+  api.perplexity.ai even when PERPLEXITY_API_BASE_URL=localhost:8765 is set and the proxy is up.
+- Sticky: _correctable (providers.py:297-309) treats the existing paid role as a user choice and
+  won't rewrite it.
+- FIX: prefer the local proxy when PERPLEXITY_API_BASE_URL is localhost:8765 (or make
+  free_proxy_first the default); always include baseURL when writing a perplexity role; treat a
+  paid-perplexity role as correctable when the free proxy is reachable.