Summary

The boot-time TOML drift loop at crates/librefang-kernel/src/kernel/mod.rs:~2860 overwrites multiple runtime-rendered prompt tails on every restart, not just the ## User Configuration block. PR #3142 fixes the settings-tail case; this issue tracks the rest.

Mechanism (recap)

At hand activation / agent spawn, the kernel APPENDS several markdown blocks to manifest.model.system_prompt:

These are persisted to the agents DB.

On every subsequent restart, the boot-time drift detector compares the disk TOML manifest to the DB blob:

let changed = serde_json::to_value(&disk_manifest).ok()
    != serde_json::to_value(&entry.manifest).ok();
if changed {
    entry.manifest = disk_manifest;     // ← clobbers ALL rendered tails
    kernel.memory.save_agent(&entry)?;
}

The disk TOML never carries any of those tails (they're runtime artifacts, never written back to the source file), so the comparison ALWAYS triggers on a hand-with-any-rendered-tail restart, and all the rendered context is silently dropped from the prompt.

What's already fixed (PR #3142)

PR #3142 introduces apply_settings_block_to_manifest(), makes it idempotent via a USER_CONFIG_TAIL_MARKER, and re-runs it inside the drift block before save_agent. The activation site is also refactored to use the same helper. Result: settings tail survives restarts.

What's still broken

After #3142 lands, restarts will still:

1. Strip ## Reference Knowledge. Agents lose access to their skill prompt_context.md content. The agent then falls back to skill_read_file({skill, path}) calls on demand if it knows what to ask for, but the discoverability summary is gone — affects which skills get considered on the first turn of each session, even when session_mode=new.

2. Strip ## Your Team. Agents lose the peer registry list, so agent_send to peers becomes "I don't know who's running" guesswork. Symptom: agent calls agent_list redundantly at the top of every session because the static peer info is no longer in the prompt.

Both are silent: no error, no warning, just degraded agent context. The bug is most visible on multi-hand setups with peer routing or skill-heavy hands.

Suggested follow-up shape

Two reasonable approaches:

A. Replicate the #3142 pattern for each rendered tail. Helpers
apply_skill_section_to_manifest() and
apply_team_section_to_manifest(), each idempotent via marker, each
called from both activation and drift sites. Pros: minimal, surgical.
Cons: multiplies the helper count; future runtime-rendered tails
(there will be more) need the same treatment.

B. Compare on a sanitized projection of the manifest that strips ALL known runtime-rendered tails before the diff. The drift block then only fires when the raw TOML truly differs from the raw DB form, ignoring rendered synthesis entirely. Pros: solves the whole class of bug at once; new rendered blocks are automatically tolerated as long as they have markers. Cons: requires defining a manifest_for_diff() projection and keeping the marker registry up to date.

I lean toward B for long-term hygiene, but A is the cheap incremental path if maintainer prefers landing fixes one at a time.

Repro (post-#3142)

A multi-agent hand with multiple skills:

# example-hand/HAND.toml
id = "example"
name = "Example"
skills = ["alpha", "beta"]   # both have non-empty prompt_context.md

[agents.worker]
name = "example-worker"
skills = ["alpha", "beta"]   # workaround for #3135

[agents.worker.model]
provider = "default"
model = "default"
system_prompt = """You are example-worker."""

librefang hand activate example
# Inspect example-worker's stored manifest — system_prompt has
#   ## User Configuration   (post-#3142: survives)
#   ## Reference Knowledge  (still gets dropped)
#   ## Your Team            (still gets dropped — if peers exist)

just restart
# Re-inspect — Reference Knowledge and Your Team blocks GONE.

Why one issue

These two follow-up cases share the exact same diagnosis as #3142 — same code path, same fix shape. Filing as one issue rather than two so reviewers can decide between (A) and (B) holistically.

Out of scope

• Fixing the runtime side of "what content goes into each rendered block" — that lives in prompt_builder.rs and is unrelated to drift.
• The [[settings]] schema or the resolve_settings rendering format (covered in fix(kernel): re-render hand [[settings]] tail after boot-time TOML drift #3142).