Simulink-optimizing-embedded-code

Release compatibility: MATLAB R2023a and later.

Iteratively improves generated C/C++ code from Simulink models by suggesting configuration, modeling, and architectural changes — then measuring the impact.

When to Use

• User asks to reduce runtime, RAM, ROM, or stack usage of generated code from a Simulink model
• User wants to optimize Embedded Coder output for a specific hardware target
• User asks to improve code efficiency metrics after code generation
• User wants an iterative optimization workflow with measurable before/after comparisons

When NOT to Use

• User wants to build or create a Simulink model from scratch (not optimization)
• User needs help with MATLAB scripts unrelated to Simulink code generation
• User wants to debug a simulation error (not a code efficiency issue)
• User is working with hand-written C/C++ code (not generated from Simulink)

Overall Workflow

Phase 1: Gather Requirements -> Confirm goal -> Decide codegen vs SIL/PIL
Phase 2: Baseline -> SIL/PIL or slbuild -> User targets functions
Phase 3: Suggest batch (Stage A/B/C/D) -> User confirms
Phase 4: Apply -> Re-measure -> Goal-Axis Gate -> Compare
Phase 3-4: Repeat until all stages exhausted
Phase 5: Finalize -> Customer report -> Stop

Phases run continuously. At each boundary the agent writes diagnostics and state to disk (see Transition Protocol), then proceeds directly to the next phase without stopping or asking the user for permission to continue.

First Action: Detect Model and Route

1. Detect open model: None open: stop; one model: use it, derive <project_path> from the model's file location; multiple: ask user.

   find_system('type','block_diagram','BlockDiagramType','model')
   

2. Check for state:

   isfile(fullfile('<project_path>', '.eco_diagnostics', 'state.json'))
   

3. Route:
   • No state.json -> Fresh run. Read Phase 1.
   • state.json exists -> Resume. Run eco_validate_state, follow NEXT_ACTION.
   • Exception: If NEXT_ACTION points to Phase 4 but workspace is clean (no partial apply), re-route to Phase 3 — the approved batch is lost and must be re-suggested.

Phase Routing Table

Phase 1 is NOT optional. Even when intent seems obvious ("just fix it"), you MUST complete Phase 1. Requirements gathering asks questions that cannot be inferred — user must confirm goal, hardware, and verification mode. Phrases like "just do it" express impatience, NOT informed consent to skip.

Read ONLY the phase file needed:

Phase	When	File to Read
1 — Gather Requirements	Fresh run	<skill_root>/references/gathering-requirements.md
2 — Baseline Measurement	After Phase 1	<skill_root>/references/measuring-model-metrics/reference.md
3 — Suggest Optimizations	After Phase 2 or 4	<skill_root>/references/suggesting-optimizations.md
4 — Apply & Re-measure	After Phase 3	<skill_root>/references/measuring-model-metrics/reference.md (remeasure mode)
5 — Finalize Results	All stages exhausted	<skill_root>/references/finalizing-results.md

Do not preload all phase files. After reading each, log:

eco_token_log('<relative_path_of_phase_file>')

On-Demand Protocol Files

Read ONLY when the situation requires:

File	When
references/protocols/correctness-gate.md	Phase 4 (after SIL/PIL re-run, before efficiency gate)
references/protocols/goal-axis-gate.md	Phase 4 (after correctness gate passes)
references/protocols/checkpointing-revert.md	Phase 4 or any revert. Also log references/evolutions-checkpoint.md
references/protocols/harness-detection.md	Phase 1 (fresh run)
references/protocols/customer-extensions.md	Phase 3 and 4 (when .custom_optimizations/ exists)

Cross-Cutting Rules

1. Confirm before acting. Never apply changes without explicit user approval. Complete Phase 1 first even if user says "just fix it".
2. Correctness before efficiency. Phase 4 runs Numerical Correctness Gate BEFORE Goal-Axis Gate. Correctness failures auto-reject. In codegen mode, per-iteration gate is skipped but Phase 5 runs mandatory final SIL verification.
3. Goal axis is inviolable. Regressions on GOAL axes -> reject and revert. TRADEOFFS only relaxes non-goal axes.
4. One checkpoint per accepted version. Taken AFTER both gates pass via eco_snapshot. Never pre-apply.
5. Delegate heavy reads to sub-tasks. Never read SIL/PIL reports or generated code in main context.
6. Always update diagnostics before transition. Decision trace + subskill log + verify token ledger non-empty. Refuse to transition without them (OR-05/OR-06).
7. Stage progression with user override. Default: A->B->C->D then Phase 5. If user wants to stop, inform of remaining stages, respect their decision, proceed to Phase 5. Auto-finalize only after all STAGE_SCOPE stages exhausted (OR-13).
8. Customer preferences are lazy-loaded. If <PROJECT_PATH>/.custom_optimizations/optimization_preferences.yaml exists, Phase 3 reads skip/know, Phase 4 reads never rules. Custom optimizations run before built-in subskills. See references/protocols/customer-extensions.md.

Transition Protocol

State Object (state.json)

Lives at <project_path>/.eco_diagnostics/state.json. Captured in every git snapshot, so prior states are recoverable via git show <sha>:.eco_diagnostics/state.json.

Shape:

{
  "MODEL": "<model_name>",
  "PROJECT_PATH": "<absolute_path_to_project>",
  "HARDWARE": "<target>",
  "BOARD_CONNECTED": true,
  "GOAL": "speed|RAM|ROM|balance|MISRA",
  "TRADEOFFS": "<constraints>",
  "VERIFICATION_MODE": "codegen|SIL|PIL",
  "PROFILING_FOCUS": "time|stack",
  "REPORT_LEVEL": "coarse|detailed",
  "ENABLE_CRL": true,
  "TOLERANCE": { "absolute": 1e-6, "relative": 0.01 },
  "SIM_STOP_TIME": "10",
  "GOLDEN_REF_PATH": "<path to .eco_diagnostics/golden_reference/<model>_golden_ref.mat>",
  "TARGET_FUNCTIONS": ["..."],
  "MODEL_FINGERPRINT": {},
  "CURRENT_STAGE": "A|B|C|D|FINALIZE",
  "STAGE_SCOPE": ["A","B","C","D"],
  "DEFERRED_LEVERS": [],
  "liveVersion": "v1",
  "versionMap": [
    { "version": "v0", "tag": "v0_pristine", "commitSHA": "...", "metrics": {},
      "status": "OK pristine", "parentVersion": null,
      "revertCause": null, "revertTargetVersion": null, "revertTargetCommitSHA": null },
    { "version": "v1", "tag": "v1_baseline", "commitSHA": "...",
      "metrics": { "ExecTime_ns": 0, "GlobalRAM_B": 0 },
      "status": "OK baseline — measurement prereqs applied", "parentVersion": "v0",
      "revertCause": null, "revertTargetVersion": null, "revertTargetCommitSHA": null }
  ],
  "LATEST_METRICS": { "ExecTime_ns": 0, "GlobalRAM_B": 0, "perTargetFunction": [] },
  "REPORT_FILE": "<path>",
  "NEXT_ACTION": "<structured action>"
}

Codegen mode NOT permitted when GOAL=speed|balance (GR-05).

Customer Preferences (NOT in state.json)

Read lazily from <PROJECT_PATH>/.custom_optimizations/optimization_preferences.yaml — not cached in state. Template at <skill_root>/assets/optimization_preferences.yaml. See protocols/customer-extensions.md.

NEXT_ACTION Format

Must use numbered sub-step format: "Phase <N> <name> — (1) READ <file>, (2) CHECKPOINT: <what>, (3) <action>, (4) AWAIT_USER: <what>". Prefixes: READ = must read file first; CHECKPOINT = must snapshot; AWAIT_USER = stop and wait for user response. Sub-steps without a prefix are autonomous actions.

Per-entry versionMap fields (all mandatory)

version (label, e.g. "v2a"), tag (human-readable), commitSHA (null only for FAIL pre-checkpoint), metrics (empty for revert leaves), status ("OK pristine" | "OK ACCEPT" | "FAIL rejected" | "USER_REVERT"), parentVersion (null for v0; after revert to v{i}, subsequent entries use v{i}), revertCause ("Gate_Rejected" | "User_Requested_Revert" | null), revertTargetVersion, revertTargetCommitSHA.

liveVersion semantics

Always read state.liveVersion, never versionMap[-1]. Advances only on accepts; reverts point it back. After v0_pristine: "v0"; after v1_baseline: "v1"; after gate PASS: the accepted version; after Gate_Rejected revert: unchanged (gate restored the parent); after User_Requested_Revert: revertTargetVersion.

What does NOT create a versionMap entry

1. User declines suggested batch at end of Phase 3.
2. In-conversation undo (inverse MATLAB op, no commitSHA ever existed).

Transition Execution Steps

Before every phase transition:

1. Append decision trace to .eco_diagnostics/eco_decision_trace.md. Steps 2-6 blocked until written.
2. Verify token ledger (token_ledger.json non-empty). Steps 3-6 blocked until verified.
3. Write updated state.json with NEXT_ACTION, CURRENT_STAGE, versionMap, LATEST_METRICS.
4. If new versionMap entry has commitSHA = null: Skip if all entries already have commitSHA.

   eco_snapshot(workspacePath, tag, description, modelName)
   

5. If step 4 ran: Re-write state.json with populated commitSHA and updated liveVersion.
6. Proceed to next phase per NEXT_ACTION.

Revert variant (Kind A/B): Steps 1, 2, 6 only — no new checkpoint.

Phase Resume

When state.json exists on invocation:

1. Read state. Parse state.json.
2. Incomplete transition check. If latest versionMap entry has commitSHA: null:
   • Tag found on HEAD -> populate commitSHA from HEAD, update liveVersion.
   • No tag + dirty tree -> complete snapshot via eco_snapshot.
   • No tag + clean tree -> remove dangling entry.
3. Validate workspace:

   addpath(fullfile('<skill_root>', 'scripts'));
   result = eco_validate_state('<PROJECT_PATH>', '<commitSHA>', '<MODEL>');
   

4. Handle result:
   • clean -> proceed. dirty + modelDirty=false -> auto-discard (git checkout -- .), log OR-09.
   • dirty + modelDirty=true -> present dirty-model options (discard or keep+re-measure).
   • head_mismatch -> present mismatch options (start fresh or restore).
   • error -> report and halt.
5. Resume from NEXT_ACTION.

Workspace Recovery

Dirty model — tell user: uncommitted model changes since last checkpoint. Options: (1) Discard changes and restore to last checkpoint, (2) Keep changes and re-measure as new baseline.

HEAD mismatch — tell user: workspace state doesn't match expected SHA. Options: (1) Start fresh from current state with re-measure, (2) Restore to last known state.

Discard: Reopen model after reset. State unchanged.

close_system('<MODEL>', 0);
clear mex; clear functions;
system('git checkout -- .');
system('git clean -fd');
open_system(fullfile('<PROJECT_PATH>', '<MODEL>.slx'));

Keep+re-measure: Append to versionMap, clear metrics, route to Phase 2.

eco_snapshot('<PROJECT_PATH>', 'v<N>_external_edit', 'External model modifications incorporated', '<MODEL>')

Restore (mismatch): State unchanged.

eco_revert('<PROJECT_PATH>', '<expectedSHA>', '<MODEL>')

Re-baseline (mismatch): Update liveVersion's commitSHA to HEAD, clear metrics, route to Phase 2.

Token Usage Tracking

Tracked via eco_token_log (uses eco_token_count). Ledger at .eco_diagnostics/token_ledger.json.

Two sources: (1) Static files — counts from <skill_root>/assets/file_token_registry.json, logged by name only. (2) Dynamic scripts — print eco_output_tokens: <N> to console; agent extracts N from MCP response text.

CRITICAL: eco_output_tokens is console output, NOT a struct field. Do NOT access as result.eco_output_tokens — it will error. Run the script in one evaluate_matlab_code call, then log in a separate call:

% WRONG — causes "Unrecognized field name" error:
detail = ecokg_detail('sug_atomic_inline');
eco_token_log('ecokg_detail', detail.eco_output_tokens);

% CORRECT — two separate evaluate_matlab_code calls:
% Call 1: run the script (console prints "eco_output_tokens: 1087")
detail = ecokg_detail('sug_atomic_inline');
disp(jsonencode(detail))

% Call 2 (separate): log the token count extracted from console output
eco_token_log('ecokg_detail', 1087)

After file reads:

eco_token_log('references/gathering-requirements.md')

After scripts (separate call):

eco_token_log('ecokg_query', N)  % N from "eco_output_tokens: N" in console output

The ledger IS the token report (OR-05). renderOptimizationReport reads it directly.

Decision Trace & Subskill Invocation Log

File: .eco_diagnostics/eco_decision_trace.md. Format: OK <ID> | WARN <ID> | SKIP <ID> with explanation. Every risk has a unique Diagnostic ID. Missing entries = never considered = diagnostic finding.

## Phase: <N> — <name>
### Skill: <path>
### Decisions Made
- <param>: <value> — <why>
### Risk Checks
- OK/WARN/SKIP <ID>: <detail>
### Suggestions Emitted (Phase 3 only)
- [S1] Stage C | "<desc>" | Blocks: [...] | Risk checks: OK SO-05, OK SO-06
### Unexpected Events
- <errors, retries, fallbacks>
### Subskill Invocation Log
- OK/SKIP <name>: <reason>

Every candidate child gets a line, even if skipped. Append at the start of every phase.

Codegen-Only Path

When VERIFICATION_MODE = codegen, Phase 2/4 use static analysis (no SIL/PIL):

1. Skip configureProfilingMode.
2. Run CodeMetricsFetcherCodegen('<model>') — normal sim (with signal logging for golden ref) + slbuild + rtw.codemetrics.CodeMetrics.
3. Read generated .c/.h directly for analysis.
4. Phase 2 saves golden reference from simOut.
5. Phase 4 skips per-iteration correctness gate.
6. Phase 5 runs mandatory SIL verification against golden ref. Exception: If state.SIL_FALLBACK = true, skip verification and omit from report.

Restriction: Codegen NOT permitted when GOAL = speed or balance (requires SIL/PIL for execution-time measurement).

Behavioral Guidelines

• Conversational iterative dialogue, not one-shot. Explain in plain language.
• Be honest about uncertainty — suggest measuring when unsure.
• Use tools, not guesses — always query actual values. Handle errors gracefully.
• Track cumulative progress via version map. Use ecokg_query for the authoritative catalog.
• Use sub-tasks for heavy reads.

Context & Token Management

Action	Where	Why
Reading SIL/PIL reports or generated code	Sub-task	Large output; keeps main window clean
Computing before/after deltas	Sub-task	Involves reading two reports
Running Goal-Axis Gate delta computation	Sub-task	Heavy metric comparison delegated
Running validate_params, configureProfilingMode	Main thread	Small output, informs next interaction
Running CodeMetricsFetcherSIL/PIL	Main thread	Capture report path, then delegate reading
Applying set_param, presenting suggestions	Main thread	Small/interactive

Rules: Never read reports/generated code in main thread. Never re-read files. Minimize tool output. Parallelize independent calls. Keep user messages concise.

Risk Table

ID	Risk	Mitigation
OR-01	Context overflow	Delegate heavy reads to sub-tasks
OR-02	Test-harness optimization	Run harness detection protocol
OR-03	Stale checkpoint	save_system then checkpoint AFTER gate passes
OR-04	codegen/SIL/PIL mismatch	Carry VERIFICATION_MODE in state; codegen blocked for speed/balance (GR-05)
OR-05	Token ledger empty	Refuse to transition until non-empty
OR-06	Decision trace missing	Refuse to transition until appended
OR-07	Goal-axis regression accepted	Run Goal-Axis Gate; ablate bundles
OR-09	Dirty workspace on resume	Run eco_validate_state; handle per Recovery Options
OR-10	Stale state after revert	Rewrite state BEFORE transition after every revert
OR-11	Diagnostic-file wipe via revert	.gitignore with .eco_diagnostics/; reconstruct from context
OR-12	Missing v1_baseline	Always take in Phase 2 after initial SIL/PIL run
OR-13	Premature finalization	Inform user of remaining stages; respect explicit stop
OR-14	Correctness regression	Run Correctness Gate before efficiency gate; auto-reject on FAIL
OR-15	Golden ref not saved	Always save in Phase 2; store path in state
OR-16	Customer preferences ignored	Check .custom_optimizations/ at Phase 3/4 entry
OR-17	Over-suppression	Warn if all subskills for GOAL are suppressed
OR-18	Custom optimization breaks model	Gates still run; auto-revert on failure
OR-19	Codegen for runtime goal	Phase 1 guardrail GR-05: explain and upgrade to SIL/PIL

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