refactor: unify agent history and harden runtime diagnostics

Preserve user guidance through history compression, stabilize Flash index targets, and retire withdrawn checks without applying stale verdicts.

Improve runtime diagnostics, tool responses, and history rendering. Simplify documentation and comments.

Validation: 2076 tests passed in the full suite; 381 affected tests and 26 frontend tests passed after cleanup. Ruff and the quality ratchet passed.

artemis/graph/perception.py

@@ -92,6 +92,29 @@ def _check_injected_instruction_file(base_dir: str) -> dict | None:
     return None
 
 
+def _unprotect_current_check_lines(ctx: ArtemisContext) -> None:
+    """Record the plan's current check lines as editable under user guidance."""
+    from artemis.utils.notes import get_note_file_path
+    from artemis.utils.plan_grammar import parse_plan
+
+    unprotected = getattr(ctx, "guidance_unprotected_checks", None)
+    if not isinstance(unprotected, set):
+        unprotected = set()
+    try:
+        plan_path = get_note_file_path(ctx.data_engine.base_dir, "task_plan")
+        text = plan_path.read_text(encoding="utf-8") if plan_path.exists() else ""
+    except Exception as e:
+        logger.warning(f"Could not read task_plan for the guidance check-line waiver: {e}")
+        text = ""
+    added = {(ci.kind, ci.text) for ci in parse_plan(text).check_items}
+    unprotected |= added
+    ctx.guidance_unprotected_checks = unprotected
+    logger.info(
+        f"User guidance received: {len(added)} declared check line(s) may now be edited"
+        " by the Operator."
+    )
+
+
 async def perception_node(state: State, ctx: ArtemisContext) -> dict:
     """Perception node (fast path): captures screenshot, extracts XML hierarchy, and performs OCR.
 
@@ -114,6 +137,14 @@ async def perception_node(state: State, ctx: ArtemisContext) -> dict:
         if injected_payload:
             injected_instruction = injected_payload.get("instruction")
             user_stop_requested = bool(injected_payload.get("release_loop"))
+            if isinstance(injected_instruction, str) and injected_instruction.strip():
+                # User guidance outranks the plan's declared standards: every
+                # check line that exists right now loses its machine
+                # restoration for the rest of the run (kept on the run context,
+                # not the per-turn State), so the Operator can drop or reword
+                # it in whichever later write it gets to it. Lines added after
+                # this moment stay protected until the next instruction.
+                _unprotect_current_check_lines(ctx)
 
     controller = UnifiedMobileController(ctx)