feat(cli+installer): codegraph explore/node CLI + instructions-file block — subagent & non-MCP reach (#704) (#819)

Task-tool subagents never see the MCP initialize instructions and hold
the MCP tools only as deferred names they rarely think to load — so
delegated work bypassed codegraph almost entirely (measured ~1 of 9
forced-delegation runs touched it; the rest did 30-50 grep/read calls).
Two additions close the gap:

- CLI: `codegraph explore` and `codegraph node` call the same ToolHandler
  as the MCP tools and print identical output — the graph for any agent
  with a shell (subagents, Gemini CLI, raw Codex, humans).
- Installer: each agent target (claude/codex/gemini/opencode) writes a
  short marker-fenced CodeGraph section into its instructions file —
  the one channel subagents DO receive — naming both surfaces. Upsert
  self-heals the stale pre-#529 long block; uninstall strips it; re-runs
  are byte-equal unchanged. (#529's duplication argument bounded the
  size: four lines, commands only.)

A/B (excalidraw, sonnet/high, forced Explore-agent delegation): without
the block, subagent codegraph usage ~1/9 runs; with it, 4/4 — subagents
ToolSearch-load the MCP tools and run explore 5-7x, best runs with ZERO
Read/grep (80-95s vs 150-197s baseline). The block's mechanism: the
parent relays the note into the task prompt, making the deferred tool
names salient.

Contract tests updated to the new expectations (write + self-heal
replace the #529 strip-only behavior); README install/guidance sections
refreshed (they also still described the pre-#817/#818 tool surface).

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

src/installer/targets/gemini.ts

@@ -38,6 +38,7 @@ import {
   readJsonFile,
   removeMarkedSection,
   writeJsonFile,
+  upsertInstructionsEntry,
 } from './shared';
 import {
   CODEGRAPH_SECTION_END,
@@ -84,11 +85,10 @@ class GeminiTarget implements AgentTarget {
     const files: WriteResult['files'] = [];
     files.push(writeMcpEntry(loc));
 
-    // GEMINI.md is no longer written — the codegraph usage guidance
-    // ships in the MCP server's `initialize` response (issue #529).
-    // Strip a block a previous install left so an upgrade self-heals.
-    const instrCleanup = removeInstructionsEntry(loc);
-    if (instrCleanup.action === 'removed') files.push(instrCleanup);
+    // GEMINI.md gets the short marker-fenced CodeGraph block (#704):
+    // subagents and non-MCP harnesses read GEMINI.md but never the MCP
+    // initialize instructions. Upsert self-heals a stale pre-#529 block.
+    files.push(upsertInstructionsEntry(instructionsPath(loc)));
 
     return { files };
   }