feat: extract relaxed structures from QE outputs and create next input

[ToAmano]

Implements the feature to extract relaxed structures from QE output log files and merge them with a template input file to generate the next calculation input (Issue #25).

Closes #25

1. Updates EspressoAdapter to auto-detect and read QE output logs using ASE's espresso-out parser (retrieving the final relaxed configuration).
2. Improves get_adapter to examine the first few lines of file contents to correctly identify QE output log files.
3. Implements the --template option in the CLI to preserve computational parameters and comments from a template input file when writing the output.
4. Implements the --calc (--calculation) option to override the calculation parameter in the QE input namelist.
5. Implements safety checks to ensure a template file is provided when converting a QE output log to a QE input file.
6. Adds comprehensive unit and integration tests covering the new features.
7. Keeps code coverage at 95%.

[cr-gpt]

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information