Fix README/doc inconsistencies (duplicate tool numbering, .env.example vs env_example.txt)

[AndreaV-Lsi]

Problem

Documentation inconsistencies in the README and env-template references:

• Duplicate tool numbering in the README tool catalog — #13 appears twice (update + delete),
  and #15–#20 repeat across the time-entry / version / membership sections, so the numbered
  list is misleading.
• .env.example vs env_example.txt — docs/config refer to .env.example, but the actual
  template file committed is env_example.txt (the .claude/config.json alwaysInclude reference
  is handled in the .claude tooling issue; this issue covers the README/user-facing references).

Scope

• README.md: renumber the tool catalog sequentially and uniquely.
• Reconcile env-template filename references so they resolve to the real file (either rename the
  file to .env.example or fix the references to env_example.txt — pick one and apply
  consistently).

Out of scope

• Content rewrites beyond numbering and the env-template filename.
• .claude/config.json (covered by the .claude tooling issue).

Acceptance criteria

• README tool numbering is sequential and unique.
• Every env-template reference resolves to a file that exists in the repo.

Type: docs, tiny/safe. Label: backlog.