fix(subprocess): register the agent system instruction in subprocess-spawned child sessions

[Brian Krabach (bkrabach)]

Summary

Subprocess-spawned agents were silently dropping their system instruction (persona). The instruction key crossed the process boundary intact inside config (via merge_configs() on the parent side), but nothing on the subprocess child path ever read it.

Root cause: Two defects, now fixed:

1. Defect 1 (shipped bug): System instruction never registered in subprocess child

   • config['instruction'] present but never consumed
   • Agent runs with NO persona at all (generic session)
   • Live in production: amplifier-bundle-dot-graph recipes use spawn_mode: subprocess

2. Defect 2 (found in review): @mention bleed-through via shared deduplicator

   • First fix version shared session's ContentDeduplicator across persona + prompt expansion
   • ContentDeduplicator.get_unique_files() returns EVERY file ever seen, re-serializes on each call
   • Persona content leaked into prompt context block (verified: 205 chars extra per turn)

Fix

For Defect 1:

In _run_child_session, resolve config.get('instruction') or config.get('system', {}).get('instruction') with an isinstance dict guard, expand @mentions, then register via:

• Preferred: set_system_prompt_factory(...) (allows composable hooks)
• Fallback: add_message({'role': 'system', ...}) (for contexts without factory)

Mirrors in-process path in amplifier-app-cli/session_spawner.py exactly.

For Defect 2:

Persona expansion now uses a fresh ContentDeduplicator() instead of sharing the session's instance, matching the already-correct pattern at amplifier_foundation/bundle/_prepared.py:411-412 ("Fresh deduplicator each call").

Verification Evidence

RED proven twice, independently:

Pre-fix probe (persona present in config, nothing registered):

AssertionError: SUBPROCESS CHILD NEVER RECEIVES THE AGENT PERSONA.
    config['instruction'] was present: 'You are ROB-PERSONA-MARKER-9x7. Always a'...
    set_system_prompt_factory awaited: 0
    add_message(role=system) calls   : 0
    => the agent runs with NO persona; it is a generic session.

Revert-production-only (tests kept):

FAILED TestChildSystemInstruction::test_system_instruction_registers_factory
FAILED TestChildSystemInstruction::test_system_instruction_fallback_add_message_when_no_factory
FAILED TestChildSystemInstruction::test_system_instruction_nested_system_dict_form
FAILED TestChildSystemInstruction::test_system_instruction_mentions_expanded
4 failed, 58 passed

Bleed-through regression test, RED-proven by reverting only the dedup line:

E       assert 'PERSONA-FILE-CONTENT-XYZ' not in '<context_fi...task.md now.'
E         'PERSONA-FILE-CONTENT-XYZ' is contained here:
E           sona.md">
E           PERSONA-FILE-CONTENT-XYZ
E           </context_file>
FAILED TestChildSystemInstruction::test_persona_mentions_do_not_bleed_into_prompt

Test suite results:

• Baseline on main: 1549 passed
• This branch: 1556 passed (+7 new persona tests)
• All tests green, zero failures

Lint: ruff check and ruff format --check both clean.

Review Trail

1. Independent code review: APPROVED, two non-blocking follow-ups (one suggested regression test, now included)
2. Council review (six lenses): 5/6 initially said DO-NOT-MERGE-YET due to potential @mention bleed-through. Executed the real dedup code and proved the bleed-through exists. The fix (fresh deduplicator) and regression test (RED-proven) are now included. All council concerns resolved.

Known Remaining Gaps

• Three hand-synced implementations of "install a persona" now exist: bundle/_prepared.py, amplifier-app-cli/session_spawner.py, and this fix. Tied together only by comments. This bug's existence IS a sync failure. Should be ticketed.
• session_spawner.py (in-process) still shares one deduplicator across its persona and instruction expansions — the same bleed-through defect, pre-existing, out of scope. Should be ticketed against amplifier-app-cli.
• Tests mocked at AmplifierSession boundary; no end-to-end subprocess run with real session included.

Files Changed

• amplifier_foundation/subprocess_runner.py — Added persona registration block in _run_child_session (after capability registration, before prompt expansion)
• tests/test_subprocess_runner.py — Added TestChildSystemInstruction class with 7 tests (factory registration, fallback path, nested form, no-instruction, @mention expansion, bleed-through regression, context-is-None no-crash)