fix: address code review findings — re-add altimate_core_rewrite, fix tool_lookup, fix skill docs

- Re-add `altimate_core_rewrite` to registry (different Rust backend from `sql_optimize`)
- Fix `tool_lookup` to use new `ToolRegistry.allInfos()` instead of fake providerID/modelID hack
- Fix `sql-review` SKILL.md: correct `altimate_core_check` params (`schema_context`, no `dialect`)
- Fix `pii-audit` SKILL.md: add `schema_index` prerequisite in Option B code block
- Add deprecation markers to 6 removed tool source files
- Fix misleading test name "tool count is exactly 80"
- Update all test REMOVED lists to exclude `altimate_core_rewrite`

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: suryaiyer95

.opencode/skills/pii-audit/SKILL.md

@@ -39,8 +39,9 @@ Analyzes column names, types, and patterns to detect PII categories:
 
 **Option B — From warehouse connection:**
 
-First inspect the schema, then classify:
+First index the schema, inspect it, then classify:
 ```
+schema_index(warehouse: <name>)
 schema_inspect(warehouse: <name>, database: <db>, schema: <schema>, table: <table>)
 schema_detect_pii(warehouse: <name>)
 ```

.opencode/skills/sql-review/SKILL.md

@@ -49,15 +49,15 @@ Call `altimate_core_check` — this is the single-call code review that composes
 - **PII exposure**: Flags queries accessing columns classified as PII
 
 ```
-altimate_core_check(sql: <sql>, schema: <schema_yaml>, dialect: <dialect>)
+altimate_core_check(sql: <sql>, schema_context: <schema_object>)
 ```
 
 ### 3. Grade the SQL
 
 Call `altimate_core_grade` to get an A-F quality score with per-category breakdown:
 
 ```
-altimate_core_grade(sql: <sql>, schema: <schema_yaml>)
+altimate_core_grade(sql: <sql>, schema_context: <schema_object>)
 ```
 
 Categories scored:

packages/opencode/src/altimate/tools/altimate-core-format.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by sql_format.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/altimate-core-is-safe.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by altimate_core_check.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/altimate-core-lint.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by altimate_core_check.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/altimate-core-optimize-for-query.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by altimate_core_prune_schema.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/altimate-core-safety.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by altimate_core_check.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/altimate-core-transpile.ts

@@ -1,3 +1,4 @@
+// DEPRECATED: Removed from registry in PR #222. Superseded by sql_translate.
 import z from "zod"
 import { Tool } from "../../tool/tool"
 import { Bridge } from "../bridge/client"

packages/opencode/src/altimate/tools/tool-lookup.ts

@@ -10,22 +10,20 @@ export const ToolLookupTool = Tool.define("tool_lookup", {
     tool_name: z.string().describe("Exact tool ID (e.g., 'sql_analyze', 'altimate_core_migration')"),
   }),
   async execute(args) {
-    const tools = await ToolRegistry.tools(
-      { providerID: "anthropic" as any, modelID: "" as any },
-      undefined,
-    )
-    const tool = tools.find((t) => t.id === args.tool_name)
-    if (!tool) {
-      const ids = tools.map((t) => t.id).sort()
+    const infos = await ToolRegistry.allInfos()
+    const info = infos.find((t) => t.id === args.tool_name)
+    if (!info) {
+      const ids = infos.map((t) => t.id).sort()
       return {
         title: "Tool not found",
         metadata: {},
         output: `No tool named "${args.tool_name}". Available tools:\n${ids.join(", ")}`,
       }
     }
 
+    const tool = await info.init()
     const params = describeZodSchema(tool.parameters)
-    const lines = [tool.id, `  ${tool.description}`, ""]
+    const lines = [info.id, `  ${tool.description}`, ""]
     if (params.length) {
       lines.push("  Parameters:")
       for (const p of params) {
@@ -37,7 +35,7 @@ export const ToolLookupTool = Tool.define("tool_lookup", {
       lines.push("  No parameters.")
     }
 
-    return { title: `Lookup: ${tool.id}`, metadata: {}, output: lines.join("\n") }
+    return { title: `Lookup: ${info.id}`, metadata: {}, output: lines.join("\n") }
   },
 })
 

packages/opencode/src/tool/registry.ts

@@ -92,6 +92,7 @@ import { AltimateCoreExportDdlTool } from "../altimate/tools/altimate-core-expor
 import { AltimateCoreFingerprintTool } from "../altimate/tools/altimate-core-fingerprint"
 import { AltimateCoreIntrospectionSqlTool } from "../altimate/tools/altimate-core-introspection-sql"
 import { AltimateCoreParseDbtTool } from "../altimate/tools/altimate-core-parse-dbt"
+import { AltimateCoreRewriteTool } from "../altimate/tools/altimate-core-rewrite"
 import { ToolLookupTool } from "../altimate/tools/tool-lookup"
 import { ProjectScanTool } from "../altimate/tools/project-scan"
 import { DatamateManagerTool } from "../altimate/tools/datamate"
@@ -236,6 +237,7 @@ export namespace ToolRegistry {
       SchemaTagsTool,
       SchemaTagsListTool,
       SqlRewriteTool,
+      AltimateCoreRewriteTool,
       SchemaDiffTool,
       AltimateCoreValidateTool,
       AltimateCoreCheckTool,
@@ -278,6 +280,11 @@ export namespace ToolRegistry {
     ]
   }
 
+  /** All tool infos without model/provider filtering. */
+  export async function allInfos(): Promise<Tool.Info[]> {
+    return all()
+  }
+
   export async function ids() {
     return all().then((x) => x.map((t) => t.id))
   }