refactor!: simplify runtime tools and remove replay engines (#572)

* fix(hopper): report unavailable procedure body coverage

* refactor!: simplify runtime tools and remove replay engines

Keep direct inspection, capture, and comparison tools. Bind handlers to named contracts and let agents compose experiments with commands and local fixture servers.

BREAKING CHANGE: Remove controlled replay, Node characterization, finite replay-machine, managed runtime planning, and redundant string-tracing tools. Retire process replay, shims, reactive scenarios, custom checkpoints, and active browser replay and origin-scope inputs.

docs/javascript-application-workflows.md

@@ -132,8 +132,10 @@ unique occurrence on each side and pairing is reciprocal. Changes use JSON
 Pointer paths with `added`, `removed`, `changed`, or `unknown` status. A missing
 field is added or removed only when the relevant parent-property coverage is
 complete on both shapes. The output includes exact selector candidates,
-omissions, Evidence links, coverage, limitations, and a separate controlled
-replay recommendation; it does not execute JavaScript.
+omissions, Evidence links, coverage, and limitations; it does not execute
+JavaScript. When runtime semantics matter, run behavioral probes directly
+against the relevant application versions and capture them through the
+available browser, Electron, or process workflows.
 
 ## CLI and verification
 
@@ -162,22 +164,10 @@ Because source Evidence and derived Evidence are retained by the normal session
 ledger, evidence bundles and analysis snapshots can carry these records without
 another persistence format.
 
-## Controlled replay boundary
+## Runtime evidence
 
-Static graph workflows never execute a graph node or recovered module.
-`run_controlled_replay` is the separate extracted-module boundary. A plan
-request and execute request share the same manifest; execution must include the
-exact plan digest, and the worker runs inside the mandatory Linux OS sandbox.
-The sandbox is an execution boundary; it does not make replay a real application
-runtime observation.
-
-Replay observations retain `controlled-replay` authority. They cannot
-promote static inference into passive runtime observation or prove that the
-original application, renderer, preload, main process, or remote service
-behaved identically.
-
-Module, explicit case, and preset-generated case lists have no fixed
-item-count ceiling. Replay plans commit the caller's resource budgets, and the
-worker protocol checks the complete request against that declared byte budget
-before probing executables or reading modules. Aggregate module-source and
-case-input bytes are likewise checked against the caller's declared budgets.
+Static graph workflows do not execute recovered code. When runtime semantics
+matter, run behavioral probes directly against the relevant application
+versions and capture them through the available browser, Electron, or process
+workflows. Those observations do not prove behavior in an unobserved app
+version or environment.