Context window balloons at fresh-session start (~40-70K baseline tokens) and full-file re-injection on every auto-compact

Environment: Claude Code 2.1.259 (macOS Darwin 24.5.0, arm64), VS Code extension 2.1.259, Sonnet 5 (Pro plan)

Summary: Two related but distinct issues, both confirmed with direct evidence from session transcript files (~/.claude/projects/*/*.jsonl), not speculation.

Issue A — Fresh-session-start baseline (~20-35% of window before any real work):
Measured the very first assistant turn's usage field across 10 independent fresh sessions (5 in one project, 5 in another): totals ranged 40,613-43,344 tokens in one project and 44,252-69,534 in another. Notably, cache_read_input_tokens was identically 7,298 across 5 separate sessions in the same project — a fixed, cached harness-level cost. No type:"file" attachments were present at session start in any sample, ruling out "recently read files" as the cause. Tried 4 fixes across earlier sessions (disabling zero-usage plugins, narrowing global MCP server scope, isolating a specific plugin's SessionStart hook, trimming personal CLAUDE.md) — none moved this baseline more than a few percent. Best available explanation (by elimination, not direct measurement): cumulative cost of per-session skill-catalog/agent-type-listing/deferred-tool-name-list/MCP-instruction injection that Claude Code sends on every session start regardless of plugin count.

Issue B — Full-file re-injection on every auto-compact:
Scanned all 92 session files in one project for isCompactSummary markers: found 42 real auto-compact events. In each, following the compact summary, Claude Code re-attaches: (1) the compact summary itself, (2) a subset of files recently touched via Read as full content (attachment.type:"file", averaging ~7.8KB per event) rather than the lightweight compact_file_reference given to other touched files, (3) deferred_tools_delta, agent_listing_delta, mcp_instructions_delta (present in 41/42 events), (4) SessionStart:compact hook output including a plugin's full skill text. This appears to be not proportional to actual new content — it's a re-send of largely-unchanged state on every single compact, which compounds over long sessions. Cross-project check: auto-compact never fired in shorter-lived project sessions (longest observed: 3,692 lines) — only in the one project with marathon 30K+ line sessions — consistent with the ~83.5% documented auto-compact threshold, but the reinjection cost itself at each compact appears avoidable/reducible.

Ask:

1. Is there a way to make compact's per-file full/reference decision configurable, or default more conservatively to references?
2. Can agent-listing/deferred-tools/MCP-instruction blocks be sent as true deltas (only what changed) instead of full resends at every compact?
3. Is the ~40-70K fixed session-start cost expected to scale with plugin/skill count, and is there a lighter-weight catalog-reference mode instead of full injection?