rea/experiments/atomic-codemode

Atomic RE through Code Mode

This is an in-progress experiment, not an integrated provider release. Branch experiment/atomic-codemode-20261016 starts at main 42fc6c53ae188978deb3bedfe88287b6b316ba22 and carries the previous atomic-facts prototype. Historical measurements in ../atomic-re-tools/ retain their original baselines. No PR or merge is intended.

The goal is a real model completing reverse-engineering questions through composable facts, with Code Mode as the calling adapter. A configured feature flag, a scripted verifier or a small response does not prove that goal.

The reference is Hex-Rays IDA MCP: an on-demand reference lookup and an execution entrypoint over a richer analysis API. This experiment uses JavaScript and a QuickJS WASM environment rather than Python in the host process. It exposes only declared static analysis capabilities. It does not add target execution, patching or GUI control.

Three boundaries own the implementation:

• provider.mjs, native-ir.mjs: existing REA native target/process owners and parsed Kuna string/reference/SSA facts, retained sources, freshness and cleanup.
• api.mjs: named, validated fact/relationship contracts and session admission. SDK callers, CLI scripts and both MCP adapters use these same methods.
• executor.mjs, server.mjs, cli.mjs: bounded JavaScript composition and presentation. No analysis is reimplemented in the execution environment.

The complete Code Mode MCP catalog is open_binary, reference, execute_javascript, close_binary. Setting REA_ATOMIC_ADAPTER=direct exposes the same fact API as facts_* MCP operations for comparison. This is a distinct experimental server; the production REA catalog is not filtered or replaced.

Use the pinned Node, an existing REA build and a caller-supplied Kuna 1.833:

npm ci --prefix experiments/atomic-codemode --ignore-scripts
node --test experiments/atomic-codemode/*.test.mjs
REA_KUNA_COMMAND=/absolute/path/to/kuna node experiments/atomic-codemode/server.mjs

The local MCP registration for real model trials is named rea-codemode. agent-trial.py --mcp-entrypoint /absolute/path/to/server.mjs --server-name rea-codemode --protocol-profile atomic --profile-parent /tmp creates an isolated configuration, home and empty working directory for the model. Shell/file tools, web search and delegation are disabled. No repository or oracle is placed in that workspace. The copied authentication file is removed with the isolated profile. Model output, actual MCP calls, original errors and usage remain in the trial directory. REA_ATOMIC_TRACE and REA_ATOMIC_EVIDENCE_DIR retain actual API calls and complete sources outside the model workspace when explicitly selected by the evaluator. The ambient environment and credentials are not logged.

Current bounds: 64 MiB guest heap, 32 KiB code and script value/error payloads, 64 host calls per execution, 120 seconds wall deadline and 2 seconds of guest synchronous execution; native requests have existing supervision, an 8 MiB capture budget and 1 GiB function-memory limit. Retained source storage is 64 MiB per target, with two resident indexes (at most 2 MiB diagnostic or 8 MiB native source each). Sources are content-digested and retained until close; explicit evaluator copies survive close. Capacity failures are explicit, not clipped facts. Leases and snapshot handles prevent cross-session joins.

Invocation context and observed source IDs are additional bounded receipt metadata; the script payload bound is not a 32 KiB whole-MCP-wire limit. A real MCP probe found that a 40,000-byte guest exception bypassed that payload policy and produced a 40,183-byte response. Oversized errors now return explicit output_budget with omission metadata. Escaping expansion is checked too; ordinary smaller errors remain intact. verify-executor.mjs confirms real MCP delivery and continued access to source Evidence collected before the exception. It measures response bytes, not model tokens or an analysis speedup. Targeted JS tests now total 42, alongside the separate real-provider and native-writer checks.

The diagnostic SSA format still has incomplete CFG and phi predecessor coverage. The opt-in native recovered IR experiment adds full recovered CFG edges, exact value/operand identities, phi incoming-edge bindings, selected values/blocks reads and derived control dependence. It requires an explicitly pinned patched engine; stock Kuna does not gain those capabilities from a wrapper. Runtime successors, memory aliases and machine-semantic equivalence remain unknown. Other providers are not yet wired to this experimental service.

The initial actual model comparison favors the focused traditional workflow. The seeded value-origin task has lower cumulative input and wall time through Code Mode, but initially exposes an IR-to-machine-path error. The revised trial correctly explains that machine path with lower observed task costs; broader claims still require more than this single seeded task.

The large SQLite VM diagnostic task also completes when its native graph exceeds capacity. Atomic direct beats Code Mode on cumulative input and wall time in that sample, and a traditional reused-project run is fastest. The actual CLI client already exposes JavaScript dispatch in every lane, regardless of requested feature flags. MCP request counts therefore do not establish fewer model rounds; the ledger now records actual model responses and client dispatch/wait calls.

instructions reads selected machine byte/decode windows through the same owner. Recovered operations use origin_address and blocks origin_start; these locations cannot be substituted for machine branch destinations. The value-origin trial demonstrates why this boundary matters. The experiment now has fourteen fact methods, still behind the same four-tool Code Mode catalog.

calls connects recovered call operations to native target specifications and separates argument SSA values from passing storage. values(is_input:true) selects retained callee inputs for exact storage comparisons. These candidate links preserve snapshot identities, missing specifications, unknown storage and runtime-binding limits. The cross-function task and oracle are fixed before its real-model trials; the graph wire format is version 3, with independent version-1 call facts.

references now selects incoming exact-address references or outgoing instruction/function references, with native kind filtering, field selection and paging. Source Evidence plus source_row identifies an occurrence. Function applicability, excluded/unattributed rows, indirect targets and discovery stay explicit. fields:[] requests only the always-retained identity columns across projection contracts. The reference question and independent oracle cover real SQLite VM aggregates and a machine call omitted from optimized IR.

bytes reads explicit virtual-address ranges as native loaded-image hex without decoding them as instructions. Batched reads preserve short reads and individual failures, with 64 KiB aggregate selected-byte capacity to bound hex/bridge growth. Complete hexdumps remain in Evidence. The original-file-offset mapping and live runtime memory remain unknown. This closes a direct byte-reading contract gap for data tables; it does not establish arbitrary memory-alias analysis.

functions provides selected name/alias/entry reads. Native snapshots report code and recovered-IR facets separately, preserving readable code when graph extraction is unavailable. Real capacity and cold/warm MCP checks are documented in native-engine.md. Whole-model costs and unequal-depth comparisons remain separate in the trial report.

The corrected SQLite comparison reaches the formatter implementation in all three interfaces. Code Mode uses fewer calls than atomic direct in that sample; a traditional run reusing its persistent whole-project cache is faster than Code Mode's fresh lease. Cache state, completed-answer coverage and actual uncached tokens must therefore accompany any cost comparison.

SDK views share immutable parsed inventories with their owner. A real SDK probe initially changed a returned string and made the next query disappear under the same Evidence ID. Freezing at the cache boundary fixes that producing rule, without copying or parsing the entire inventory for each read. verify-sdk.mjs checks the real provider's string/metadata/function views and complete retained source digest. The fixed probe passes under the bounded runner (1.328 seconds, 1.144 family CPU seconds, 110.6 MiB kernel family peak, zero OOM kills and verified payload cleanup); it is a correctness check, not a model-cost measurement.

Encoded size is another real coverage boundary: two SQLite functions initially lose even their C because pretty JSON exceeds transport capacity. The native patch now uses bounded compact serialization and a graph-only failure when needed. Parser's full graph fits; Pragma retains identical C with an explicit missing graph. The 8 MiB bound remains. See the exact sizes, rebuilt engine digest and verification scope in native-engine.md.

Completion requires actual model Code Mode use, independently checked task answers, shared atomic/direct/Code Mode semantics, needed relation coverage, failure/cancellation/identity tests, and equivalent completed-task measurements including discovery/retries, actual model usage, cold/warm analysis, CPU and process-family peak memory. Negative cases such as the small SQLite function must remain in the comparison.

The outgoing-reference real-model pair now completes with identical required facts and explicit coverage limits. In its single sample, Code Mode uses 264,680 cumulative input / 93.837 seconds versus direct's 285,086 / 106.183. The shared CLI/API also verifies the VM aggregates on unpatched stock Kuna 1.833. These are scoped positive results alongside the earlier mixed adapter comparisons, not proof of general superiority. Details and retained failed/partial attempts are in trials.md.

Recovered calls and their boundary values now survive full-graph capacity failure. The real VM capture preserves 416 call operations and 1,294 boundary values while its graph remains unavailable. Values clearly state their partial scope; definition IDs do not imply readable defining operations. See the boundary question and oracle for the next pinned model task.