docs: clarify which workspace files are injected into context window (#12909)

The system prompt docs listed bootstrap files but omitted MEMORY.md,
which IS injected when present. This led users to assume memory files
are on-demand only and not consuming context tokens.

Changes:
- Add MEMORY.md to the bootstrap file list
- Note that all listed files consume tokens on every turn
- Clarify that memory/*.md daily files are NOT injected (on-demand only)
- Document sub-agent bootstrap filtering (AGENTS.md + TOOLS.md only)

Closes #12909

docs/concepts/system-prompt.md

@@ -59,11 +59,24 @@ Bootstrap files are trimmed and appended under **Project Context** so the model
 - `USER.md`
 - `HEARTBEAT.md`
 - `BOOTSTRAP.md` (only on brand-new workspaces)
+- `MEMORY.md` (when present in the workspace)
+
+All of these files are **injected into the context window** on every turn, which
+means they consume tokens. Keep them concise — especially `MEMORY.md`, which can
+grow over time and lead to unexpectedly high context usage and more frequent
+compaction.
+
+> **Note:** `memory/*.md` daily files are **not** injected automatically. They
+> are accessed on demand via the `memory_search` and `memory_get` tools, so they
+> do not count against the context window unless the model explicitly reads them.
 
 Large files are truncated with a marker. The max per-file size is controlled by
 `agents.defaults.bootstrapMaxChars` (default: 20000). Missing files inject a
 short missing-file marker.
 
+Sub-agent sessions only inject `AGENTS.md` and `TOOLS.md` (other bootstrap files
+are filtered out to keep the sub-agent context small).
+
 Internal hooks can intercept this step via `agent:bootstrap` to mutate or replace
 the injected bootstrap files (for example swapping `SOUL.md` for an alternate persona).