refactor!: remove the Graphify integration

[jeremy-wayland]

Removes Graphify Phase 1 (shipped v0.4.0) in full. Every signal it provided is already available from the GitNexus/MDG graph Topos loads for COMPOSABLE, usually at better fidelity: full startLine/endLine spans instead of point anchors, a first-class Community node label with MEMBER_OF edges instead of a bare Louvain field, and a continuous confidence: f64 + reason instead of a three-value enum. It had no production consumer, no CI coverage, and no agent-facing recommendation, and it wrapped a pre-1.0 external tool with a documented history of schema breaks.

Closes #325

What was removed

File	Lines
topos/engine/src/adapters/graphify.rs	402
topos/engine/src/graphs/graphify/{mod,models,object}.rs	494
topos/engine/src/functors/probes/graphify/{mod,orphans}.rs	185
topos/cli/src/commands/graphify.rs + graphify/{generate,orphans}.rs	371
topos/mcp/src/tools/graphify.rs	126
graphify slice of topos/mcp/src/tools/refactor.rs	217
GenerateGraphify* schemas, RefactorTargetKind::Graphify, graphify_dir	~40
resolve_graphify_dir (topos/mcp/src/evaluation/mod.rs)	23
Rust total	1,903 deleted / 34 added

Whole diff: 39 files, 156 insertions, 2,161 deletions.

Also removed: TOPOS_GRAPHIFY_TIMEOUT and GRAPHIFY_OUT handling, the graphify-out/ .gitignore entry, and the two metrics_never_leaks_graphify_keys guards in graphs/{cfg,mdg}/object.rs — they protected against a leak that can no longer happen.

Public-surface changes (breaking)

• MCP tool topos_generate_graphify_graph removed. No replacement; nothing else generated that graph. Clients calling it break.
• topos_refactor(target="graphify") removed, along with the graphify_dir parameter and the graphify_orphan / graphify_fragile_edge hotspot kinds. graphify is now rejected as an invalid enum value.
• CLI topos graphify generate|orphans removed. topos graphify now errors as an unknown subcommand.

Tool count and context budget

	Before	After
MCP tools	18	17
Tool-definition wire surface	39,584 chars (~9,896 tok)	38,668 chars (~9,667 tok)
TOTAL_CEILING_CHARS ratchet	40,500	39,500
Resources	7	7 (unchanged)
Prompts	1	1 (unchanged)

The ratchet in topos/mcp/src/context_budget.rs was moved down, keeping the repo's existing ~2% headroom convention. Every agent session pays for the tool-definition wire format on every request, so this is a permanent context saving.

Verification

• cargo test --workspace — 608 passed, 0 failed (engine 341, cli 155 + 9, mcp 103)
• cargo clippy --workspace --all-targets -- -D warnings — clean
• cargo fmt --all -- --check — clean
• cargo build --workspace; topos --help lists 10 commands with no graphify, and topos graphify errors with unrecognized subcommand 'graphify'
• stdio smoke test (initialize → tools/list / resources/list / prompts/list against topos mcp): 17 tools, topos_generate_graphify_graph absent, the substring graphify absent from the entire serialized tool surface, 7 resources, 1 prompt

grep -ri graphify across the repo (excluding openwiki/, .git/) returns only the deliberate historical references: the ## Removed target section in docs/decisions/refactor-suite.md, the ratchet's explanatory doc comment, and the new changelog entry.

Docs

Graphify content stripped from README.md, docs/source/{cli,agents,measures,installation,architecture}.rst, skills/topos/SKILL.md, topos/mcp/docs/content/{workflows,agent-contract}.md, and .agents/AGENTS.md. docs/decisions/refactor-suite.md keeps its three surviving targets and gains a Removed target section recording the rationale; its stale Python-era crates/topos-* paths are corrected to the actual topos/{engine,mcp,cli}/ layout while in there. openwiki/ and root AGENTS.md were deliberately left alone — both regenerate.

Notes

• The one-release deprecation norm (worst_files, leaf_composable_zeros) was deliberately skipped, per the issue's recommendation: zero evidence of use, and a deprecation period would keep paying the context-budget cost that is the main benefit here.
• methods: Graphify Phase 2 — robust integration, inflation/drift measures, and agent workflow #237 and methods: Graphify-backed NAVIGABLE refactoring guidance #316 should be closed as superseded when this merges.

🤖 Generated with Claude Code

[sgathrid]

lgtm!

Moving forward, can you resolve merge CHANGELOG.md conflicts? pretty garbage as when I resolve, PR then requires a re-review per the rules. Overriding + merging manually for this one.