Rewrite README and add canonical CLI reference

docs/cli.md

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+# Audita CLI Reference
+
+## Shortest Useful Command
+
+```sh
+audita process <transcript.json> --glossary <glossary.yaml> --output <corrected.json>
+```
+
+This command validates input files, runs the configured correction pipeline, and writes corrected transcript JSON.
+
+## Command Overview
+
+- `audita process`: process one transcript JSON file.
+- `audita config validate`: validate a versioned YAML config file.
+- `audita config print-effective`: print redacted effective config JSON.
+
+General help:
+
+```sh
+audita --help
+audita process --help
+audita config --help
+```
+
+## `process`
+
+Usage:
+
+```sh
+audita process <transcript.json> [flags]
+```
+
+Input requirements:
+- exactly one transcript JSON positional argument is required;
+- `--glossary <path>` is required.
+
+Config path selection for `process`:
+1. `--config <path>`
+2. `AUDITA_CONFIG`
+3. `/usr/local/etc/audita/config.yml` (if present)
+4. `/etc/audita/config.yml` (if present)
+
+For precedence and full config schema, see [`docs/config.md`](config.md).
+
+### `process` Flag Reference
+
+Core I/O flags:
+- `--config <path>`: path to versioned YAML config file.
+- `--glossary <path>`: glossary YAML input path (required).
+- `--output <path>`: corrected transcript JSON output file path.
+- `--report-json <path>`: machine-readable report JSON output path.
+- `--output-schema <key>`: output schema key (`bare-segments` or `audita-v1`).
+- `--modules <csv>`: comma-separated module sequence override.
+
+Primary LLM flags:
+- `--llm-api-key <value>`: primary LLM API key.
+- `--model <name>`: primary LLM model name.
+- `--base-url <url>`: primary OpenAI-compatible base URL.
+- `--llm-timeout-seconds <int>`: primary timeout in seconds.
+- `--max-retries <int>`: primary structured-output retries.
+
+Validation LLM flags:
+- `--validation-llm-api-key <value>`: validation LLM API key.
+- `--validation-model <name>`: validation LLM model name.
+- `--validation-base-url <url>`: validation OpenAI-compatible base URL.
+- `--validation-llm-timeout-seconds <int>`: validation timeout in seconds.
+- `--validation-max-retries <int>`: validation structured-output retries.
+- `--validation-max-prompt-tokens <int>`: validation max prompt tokens.
+
+Concurrency flags:
+- `--total-llm-concurrency <int>`: total concurrent proposal+validation LLM calls.
+- `--proposal-llm-concurrency <int>`: concurrent proposal-generation LLM calls.
+- `--validation-llm-concurrency <int>`: concurrent validation LLM calls.
+- `--llm-concurrency <int>`: alias for `--total-llm-concurrency`.
+
+Chunking and normalization flags:
+- `--target-sections <int>`: target number of transcript sections.
+- `--max-section-tokens <int>`: maximum section tokens.
+- `--min-section-tokens <int>`: minimum section tokens.
+- `--normalize-max-segment-gap <float>`: maximum same-speaker merge gap.
+- `--normalize-ellipsis-gap <float>`: gap threshold for ellipsis insertion.
+- `--normalize-max-segment-duration <float>`: maximum merged segment duration.
+- `--normalize-max-segment-tokens <int>`: maximum merged segment token estimate.
+
+Threshold flags:
+- `--glossary-confidence-threshold <float>`
+- `--homophones-confidence-threshold <float>`
+- `--spoken-word-confidence-threshold <float>`
+- `--grammar-confidence-threshold <float>`
+
+Context and diagnostics flags:
+- `--transcript-description <text>`: background context for prompts; does not override transcript content.
+- `--work-dir <path>`: per-run diagnostics work directory.
+- `--work-dir-retention <auto|always|never>`: run-directory retention policy.
+
+### `process` Output and Exit Behavior
+
+- With `--output`: stdout is expected to be empty on success.
+- Without `--output`: stdout contains transcript JSON only on success.
+- `--report-json` writes a file and is never printed to stdout.
+- Stderr is human-readable diagnostics/errors.
+- On failures after diagnostics initialization, stderr includes the diagnostics directory path.
+
+Exit behavior:
+- `0`: success.
+- `1`: runtime failure during processing/reporting/output paths.
+- `2`: CLI usage or configuration input error.
+
+### `process` Examples
+
+Write corrected transcript to a file:
+
+```sh
+audita process transcript.json \
+  --glossary glossary.yaml \
+  --output corrected.json
+```
+
+Emit transcript JSON to stdout:
+
+```sh
+audita process transcript.json --glossary glossary.yaml
+```
+
+Use explicit config and write report JSON:
+
+```sh
+audita process transcript.json \
+  --glossary glossary.yaml \
+  --config audita.yml \
+  --output corrected.json \
+  --report-json report.json
+```
+
+Override the module sequence:
+
+```sh
+audita process transcript.json \
+  --glossary glossary.yaml \
+  --modules glossary,homophones,grammar \
+  --output corrected.json
+```
+
+## `config validate`
+
+Usage:
+
+```sh
+audita config validate --config <path>
+```
+
+Behavior:
+- validates defaults merged with file config;
+- does not apply environment overrides;
+- prints `config is valid` on success.
+
+Errors:
+- `--config` is required;
+- positional arguments are rejected;
+- validation failures are printed to stderr.
+
+## `config print-effective`
+
+Usage:
+
+```sh
+audita config print-effective [--config <path>]
+```
+
+Config path selection:
+1. `--config <path>` when provided
+2. `AUDITA_CONFIG`
+3. `/usr/local/etc/audita/config.yml` (if present)
+4. `/etc/audita/config.yml` (if present)
+
+Behavior:
+- merges defaults, optional config file, and environment overrides;
+- prints redacted JSON to stdout.
+
+Errors:
+- positional arguments are rejected;
+- resolution or parse failures are printed to stderr.