Rebuild: rules:signatures, and voyager 1's 29 learned garbage signatures

rules:signatures publishes a rule set version whose dropped signatures
come from a file of tool<TAB>group lines (--add to add to the current
ones). database/data/voyager1_signatures.tsv: voyager 1's dropped ones
(>=100 probes, <=0.5% named), with their probe counts; the two builds
name the posting tools the same way.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

commands/rules_signatures.ts

@@ -0,0 +1,52 @@
+import { BaseCommand, args, flags } from '@adonisjs/core/ace'
+import type { CommandOptions } from '@adonisjs/core/types/ace'
+import { readFile } from 'node:fs/promises'
+import RuleSets from '#services/rule_sets'
+import { signatureKey } from '#lib/rules/index'
+
+/**
+ * Sets the dropped upload signatures (REBUILD.md, rules and recovery) from a
+ * file of "tool<TAB>group" lines, e.g. voyager 1's learned ones:
+ *
+ *   psql … -At -F $'\t' -c "SELECT tool, group_name FROM upload_signatures WHERE dropped"
+ *
+ * Publishes a new rule set version (ranges record the version they ran with).
+ */
+export default class RulesSignatures extends BaseCommand {
+  static commandName = 'rules:signatures'
+  static description = 'Publishes a rule set with the dropped upload signatures from a file'
+  static options: CommandOptions = { startApp: true }
+
+  @args.string({ description: 'File of "tool<TAB>group" lines (more columns and # lines are ignored), e.g. database/data/voyager1_signatures.tsv' })
+  declare file: string
+
+  @flags.string({ description: 'Note stored with the rule set version' })
+  declare note?: string
+
+  @flags.boolean({ description: 'Add to the current signatures instead of replacing them' })
+  declare add: boolean
+
+  async run() {
+    const lines = (await readFile(this.file, 'utf8')).split('\n').map((l) => l.trim()).filter((l) => l && !l.startsWith('#'))
+    const signatures = new Set<string>()
+    for (const line of lines) {
+      const [tool, group] = line.split('\t')
+      if (!tool || !group) throw new Error(`Not "tool<TAB>group": ${line}`)
+      signatures.add(signatureKey(tool, group))
+    }
+    const { version: _v, priorities: _p, ...current } = await RuleSets.current()
+    const before = new Set(current.droppedSignatures)
+    const next = this.add ? new Set([...before, ...signatures]) : signatures
+    if (next.size === before.size && [...next].every((s) => before.has(s))) {
+      this.logger.info(`Unchanged: ${before.size} dropped signatures already.`)
+      return
+    }
+    const version = await RuleSets.publish(
+      { ...current, droppedSignatures: [...next].sort() },
+      this.note ?? `${next.size} dropped signatures from ${this.file}`
+    )
+    const added = [...next].filter((s) => !before.has(s)).length
+    const removed = [...before].filter((s) => !next.has(s)).length
+    this.logger.info(`Rule set ${version}: ${next.size} dropped signatures (${added} added, ${removed} removed).`)
+  }
+}