In response to JBE's answer, Clinton could argue that the rule change in 2006 would not apply to his eligibility to run for President of France since his eligibility (if any) occurred prior to the rule change. Any rule change with retroactive effect would constitute ex post facto legal application.
https://www.law.cornell.edu/wex/ex_post_facto
According to Wikipedia, in France, so-called "lois rétroactives" (retroactive laws) are technically prohibited by Article 2 of the Code Civil, which states that: "Legislation provides only for the future; it has no retrospective operation."
See: https://www.legifrance.gouv.fr/download/pdf/legiOrKali?id=LEGITEXT000006070721.pdf&size=1,3%20Mo&pathToFile=/LEGI/TEXT/00/00/06/07/07/21/LEGITEXT000006070721/LEGITEXT000006070721.pdf&title=Code%20civil
While Wikipedia goes on to state that "[i]n practice, however, since the Code Civil does not have the status of constitutional legislation and can therefore be overruled by subsequent laws, [and that] the Conseil Constitutionnel has determined that retroactive laws can be passed within certain limits," these typically apply, according to Wikipedia, to tax or financial legislation.
See: https://web.archive.org/web/20130123221048/https://www.conseil-constitutionnel.fr/conseil-constitutionnel/francais/a-la-une/janvier-2013-la-retroactivite-fiscale-dans-la-jurisprudence-du-conseil-constitutionnel.135573.html
Clinton could argue that tax and financial legislation, neither includes, nor is related to, laws concerning eligibility for running for President of France. Indeed law regarding running for President of France is well outside the rubric of tax and financial legislation.
Furthermore, since the French Constitution provides for the election of a President, the changes in the civil code should be read in the context of Constitutional law. As such, Clinton could argue that such context strongly militates against the application of the law change ex post facto.
In sum, if Clinton had eligibility to run for President prior to the change in the civil code, it appears that he would have a bone fide tenable argument for his present eligibility, notwithstanding the rule change given that such rule change cannot apply to him ex post facto.
In conclusion, the law governing this matter, and Clinton's eligibility, is unclear to me.